Soybean variety XB39AE12

ABSTRACT

A novel soybean variety, designated XB39AE12 is provided. Also provided are the seeds of soybean variety XB39AE12, cells from soybean variety XB39AE12, plants of soybean XB39AE12, and plant parts of soybean variety XB39AE12. Methods provided include producing a soybean plant by crossing soybean variety XB39AE12 with another soybean plant, methods for introgressing a transgenic trait, a mutant trait, and/or a native trait into soybean variety XB39AE12, methods for producing other soybean varieties or plant parts derived from soybean variety XB39AE12, and methods of characterizing soybean variety XB39AE12. Soybean seed, cells, plants, germplasm, breeding lines, varieties, and plant parts produced by these methods and/or derived from soybean variety XB39AE12 are further provided.

FIELD OF INVENTION

This invention relates generally to the field of soybean breeding,specifically relating to a soybean variety designated XB39AE12.

BACKGROUND

The present invention relates to a new and distinctive soybean varietydesignated XB39AE12, which has been the result of years of carefulbreeding and selection in a comprehensive soybean breeding program.There are numerous steps in the development of any novel, desirablesoybean variety. Plant breeding begins with the analysis and definitionof problems and weaknesses of the current germplasm, the establishmentof program goals, and the definition of specific breeding objectives.The next step is selection of germplasm that possess the traits to meetthe program goals. The breeder's goal is to combine in a single varietyan improved combination of desirable traits from the parental germplasm.These important traits may include, but are not limited to: higher seedyield, resistance to diseases and/or insects, tolerance to droughtand/or heat, altered fatty acid profile(s), abiotic stress tolerance,improvements in compositional traits, and better agronomiccharacteristics.

These product development processes, which lead to the final step ofmarketing and distribution, can take from six to twelve years from thetime the first cross is made until the finished seed is delivered to thefarmer for planting. Therefore, development of new varieties is atime-consuming process that requires precise planning, efficient use ofresources, and a minimum of changes in direction.

Soybean (Glycine max) is an important and valuable field crop. Thus, acontinuing goal of soybean breeders is to develop stable, high yieldingsoybean varieties that are agronomically sound. The reasons for thisgoal are to maximize the amount of grain produced on the land used andto supply food for both animals and humans. To accomplish this goal, thesoybean breeder must select and develop soybean plants that have thetraits that result in superior varieties.

The soybean is the world's leading source of vegetable oil and proteinmeal. The oil extracted from soybeans is used for cooking oil,margarine, and salad dressings. Soybean oil is composed of saturated,monounsaturated, and polyunsaturated fatty acids. It has a typicalcomposition of 11% palmitic, 4% stearic, 25% oleic, 50% linoleic, and 9%linolenic fatty acid content (“Economic Implications of Modified SoybeanTraits Summary Report”, Iowa Soybean Promotion Board & American SoybeanAssociation Special Report 92S, May 1990). Changes in fatty acidcomposition for improved oxidative stability and nutrition are alsoimportant traits.

Industrial uses for processed soybean oil include ingredients forpaints, plastics, fibers, detergents, cosmetics, and lubricants. Soybeanoil may be split, inter-esterified, sulfurized, epoxidized, polymerized,ethoxylated, or cleaved. Designing and producing soybean oil derivativeswith improved functionality, oliochemistry, is a rapidly growing field.The typical mixture of triglycerides is usually split and separated intopure fatty acids, which are then combined with petroleum-derivedalcohols or acids, nitrogen, sulfonates, chlorine, or with fattyalcohols derived from fats and oils.

Soybean is also used as a food source for both animals and humans.Soybean is widely used as a source of protein for animal feeds forpoultry, swine, and cattle. During processing of whole soybeans, thefibrous hull is removed and the oil is extracted. The remaining soybeanmeal is a combination of carbohydrates and approximately 50% protein.

For human consumption soybean meal is made into soybean flour which isprocessed to protein concentrates used for meat extenders or specialtypet foods. Production of edible protein ingredients from soybean offersa healthy, less expensive replacement for animal protein in meats anddairy products.

SUMMARY

A novel soybean variety, designated XB39AE12 is provided. Also providedare the seeds of soybean variety XB39AE12, cells from soybean varietyXB39AE12, plants of soybean XB39AE12, and plant parts of soybean varietyXB39AE12. Methods provided include producing a soybean plant by crossingsoybean variety XB39AE12 with another soybean plant, methods forintrogressing a transgenic, a mutant trait, and/or a native trait intosoybean variety XB39AE12, methods for producing other soybean varietiesor plant parts derived from soybean variety XB39AE12, and methods ofcharacterizing soybean variety XB39AE12. Soybean seed, cells, plants,germplasm, breeding lines, varieties, and plant parts produced by thesemethods and/or derived from soybean variety XB39AE12 are furtherprovided.

DEFINITIONS

Certain definitions used in the specification are provided below. Alsoin the examples which follow, a number of terms are used. In order toprovide a clear and consistent understanding of the specification andclaims, the following definitions are provided:

AERBLT=AWB=AERIAL WEB BLIGHT. Aerial web blight is caused by the fungusRhizoctonia solani, which can also cause seedling blight and root rot ofsoybeans. Stems, flowers, pods, petioles, and leaves are susceptible toformation of lesions. Tolerance to Aerial Web Blight is rated on a scaleof 1 to 9, relative to known checks, with a score of 1 beingsusceptible, and a score of 9 being tolerant. Preliminary scores arereported as double digits, for example ‘55’ indicates a preliminaryscore of 5 on the scale of 1 to 9.

ALLELE. Any of one or more alternative forms of a genetic sequence. In adiploid cell or organism, the two alleles of a given sequence typicallyoccupy corresponding loci on a pair of homologous chromosomes.

ANTHESIS. The time of a flower's opening.

ANTHRACNOSE. Anthracnose is a fungal disease commonly caused byColletotrichum truncatum, and in some cases other Colletotrichum speciesmay be involved. The fungus produces crowded, black acervuli on infectedtissues. These dark bodies typically look like pin cushions on thetissue surface when viewed under magnification. The most common symptomsare brown, irregularly shaped spots on stem, pods and petioles.Resistance is visually scored on a range from 1 to 9 comparing allgenotypes in a given experiment. A score of 9 indicates that there is noinfection (resistance). Preliminary scores are reported as doubledigits, for example ‘55’ indicates a preliminary score of 5 on the scaleof 1 to 9.

APHID ANTIBIOSIS. Aphid antibiosis is the ability of a variety to reducethe survival, growth, or reproduction of aphids that feed on it.Screening scores are based on the ability of the plant to decrease therate of aphid reproduction. Plants are compared to resistant andsusceptible check plants grown in the same experiment. Scores of1=susceptible, 3=below average, 5=average, 7=above average, and9=exceptional tolerance. Preliminary scores are reported as doubledigits, for example ‘55’ indicates a preliminary score of 5 on the scaleof 1 to 9.

APHID ANTIXENOSIS. Aphid antixenosis is a property of a variety toreduce the feeding of aphids upon the plant, this is also known asnonpreference. Screening scores are based on the ability of the plant todecrease the rate of aphid reproduction. Plants are compared toresistant and susceptible check plants grown in the same experiment.Scores of 1=susceptible plants covered with aphids, plants may showsevere damage such as stunting and/or necrosis, equivalent or worse whencompared to susceptible check, 3=below average, plants show major damagesuch as stunting and/or foliar necrosis, 5=moderately susceptible,7=above average, about 50 aphids on the plant, plant does not exhibitsigns of plant stress, and 9=exceptional tolerance, very few aphids onthe plant, equivalent or better when compared to a resistant check.Preliminary scores are reported as double digits, for example ‘55’indicates a preliminary score of 5 on the scale of 1 to 9.

BACKCROSSING. Process in which a breeder crosses a donor parent varietypossessing a desired trait or traits to a recurrent parent variety(which is agronomically superior but lacks the desired level or presenceof one or more traits) and then crosses the resultant progeny back tothe recurrent parent one or more times. Backcrossing can be used tointroduce one or more desired traits from one genetic background intoanother background that is lacking the desired traits.

BREEDING. The genetic manipulation of living organisms, includingapplication of one or more agricultural and/or biotechnological tools,methods and/or processes to create useful new distinct varieties.

BU/A=Bushels per Acre. The seed yield in bushels/acre is the actualyield of the grain at harvest.

BROWN STEM ROT=BSR=Brown Stem Rot Tolerance. This is a visual diseasescore from 1 to 9 comparing all genotypes in a given test. The score isbased on symptoms on leaves and/or stems such as yellowing, necrosis,and on inner stem rotting caused by Phialophora gregata. A score of 1indicates severe symptoms of leaf yellowing and necrosis. Increasingvisual scores from 2 to 8 indicate additional levels of tolerance, whilea score of 9 indicates no symptoms. Preliminary scores are reported asdouble digits, for example ‘55’ indicates a preliminary score of 5 onthe scale of 1 to 9.

BSRLF=Brown Stem Rot disease rating based solely on leaf diseasesymptoms. This is a visual disease score from 1 to 9 comparing allgenotypes in a given test. A score of 1 indicates severe leaf yellowingand necrosis. Increasing visual scores from 2 to 8 indicate additionallevels of tolerance, while a score of 9 indicates no leaf symptoms.Preliminary scores are reported as double digits, for example ‘55’indicates a preliminary score of 5 on the scale of 1 to 9.

BSRSTM=Brown Stem Rot disease rating based solely on stem diseasesymptoms. This is a visual disease score from 1 to 9 comparing allgenotypes in a given test. A score of 1 indicates severe necrosis on theinner stem tissues. Increasing visual scores from 2 to 8 indicateadditional levels of tolerance, while a score of 9 indicates no innerstem symptoms. Preliminary scores are reported as double digits, forexample ‘55’ indicates a preliminary score of 5 on the scale of 1 to 9.

CELL. Cell as used herein includes a plant cell, whether isolated, intissue culture, or incorporated in a plant or plant part.

CERK=CERCOSPORA TOLERANCE. A fungal disease caused by Cercosporakukuchii which can be identified by symptoms including one or more ofmottled reddish-purple discoloration of the uppermost leaves of thesoybean plant, mottled discoloration of leaf petioles, mottleddiscoloration of pods, and/or purple discoloration of the seed coat.Infected seed, having a purple discoloration, is commonly referred to aspurple seed stain. For the multiple expressions of this disease, plantsor plant parts are visually scored from 1 to 9 relative to picturediagrams for each trait. A score of 1 indicates severity of expression,while a score of 9 indicates no symptoms. Preliminary scores arereported as double digits, for example ‘55’ indicates a preliminaryscore of 5 on the scale of 1 to 9.

CRDC=CHARCOAL ROT DROUGHT COMPLEX. A fungal disease caused byMacrophomina phaseolina that is enhanced by hot and dry conditions,especially during reproductive growth stages. Tolerance score is basedon field observations of the comparative ability to tolerate drought andlimit losses from charcoal rot infection among various soybeanvarieties. A score of 1 indicates severe charcoal rot on the roots anddark microsclerotia on the lower stem causing significant plant death.Increasing visual scores from 2 to 8 indicate additional levels oftolerance, while a score of 9 indicates no lower stem and/or root rotand no visual symptoms. Preliminary scores are reported as doubledigits, for example ‘55’ indicates a preliminary score of 5 on the scaleof 1 to 9.

CHLORIDE SALT TOLERANCE. This is a measure of the chloride saltconcentration in seedling plant tissue, arrayed on a scale based onchecks, and scores applied from 1 to 9. The higher the score the lowerthe concentration of chloride salts in the tissue measured. Preliminaryscores are reported as double digits, for example ‘55’ indicates apreliminary score of 5 on the scale of 1 to 9.

CW=Canopy Width. This is a visual observation of the canopy width whichis scored from 1 to 9 comparing all genotypes in a given test. A scoreof 1=very narrow, while a score of 9=very bushy.

CNKST=SOUTHERN STEM CANKER TOLERANCE. This is a visual disease scorefrom 1 to 9 comparing genotypes to standard checks chosen to arraydifferences. The score is based upon field reaction to the disease. Thecausative agent is Diaporthe phaseolorum var. meridionalis (SouthernStem Canker), which tends to impact southern geographic regions. A scoreof 1 indicates susceptibility to the disease, whereas a score of 9indicates the line is resistant to the disease. Preliminary scores arereported as double digits, for example ‘55’ indicates a preliminaryscore of 5 on the scale of 1 to 9.

CNKSG=SOUTHERN STEM CANKER GENETIC. This is a visual disease score from1 to 9 comparing genotypes to standard checks chosen to arraydifferences. The score is based upon toothpick bioassay in (1) field orshade tent bioassays or (2) controlled environmental chambers, and isbased on genetics that infers resistance or susceptibility to SouthernStem Canker. Diaporthe phaseollorum var. meridionalis is the causativeagent. A score of 1 indicates severe stem canker lesions, relative toknown susceptible check varieties, whereas a score of 9 indicates nomeaningful disease symptoms, consistent with known resistant checkvarieties. Preliminary scores are reported as double digits, for example‘99’ indicates a preliminary score of 9 on the scale of 1 to 9.

COTYLEDON. A cotyledon is a type of seed leaf. The cotyledon containsthe food storage tissues of the seed.

CROSS-POLLINATION. Fertilization by the union of two gametes fromdifferent plants.

DIPLOID. A cell or organism having two sets of chromosomes.

DM=DOWNY MILDEW. A fungal disease caused by Peronospora manshurica insoybean. Symptoms first appear on leaves, which can spread to podswithout obvious external symptoms, and further spread to seed. Infectedseed may have a dull white appearance. The tolerance score is based onobservations of symptoms on the leaves of plants regarding leaf damageand/or level of infection. On a scale of 1 to 9, a score of 1 indicatessevere symptoms, whereas a score of 9 indicates no disease symptoms.Preliminary scores are reported as double digits, for example ‘55’indicates a preliminary score of 5 on the scale of 1 to 9.

ELITE VARIETY. A variety that is sufficiently homozygous and homogeneousto be used for commercial grain production. An elite variety may also beused in further breeding.

EMBRYO. The embryo is the small plant contained within a mature seed.

EMGSC=Emergence Score=Field Emergence. A score based upon speed andstrength of emergence at sub-optimal conditions. Rating is done at theunifoliate to first trifoliate stages of growth. A score using a 1 to 9scale is given, with 1 being the poorest and 9 the best. Scores of 1, 2,and 3=degrees of unacceptable stands; slow growth and poor plant health.Scores of 4, 5, 6=degrees of less than optimal stands; moderate growthand plant health. Scores of 7, 8, 9=degrees of optimal stands; vigorousgrowth and plant health.

FEC=Iron-deficiency Chlorosis. Plants are scored 1 to 9 based on visualobservations. A score of 1 indicates the plants are dead or dying fromiron-deficiency chlorosis, a score of 5 means plants have intermediatehealth with some leaf yellowing, and a score of 9 means no stunting ofthe plants or yellowing of the leaves. Preliminary scores are reportedas double digits, for example ‘55’ indicates a preliminary score of 5 onthe scale of 1 to 9.

FEY=FROGEYE LEAF SPOT. This is a visual fungal disease score from 1 to 9comparing all genotypes in a given trial to known resistant andsusceptible checks in the trial. The score is based upon the number andsize of leaf lesions. A score of 1 indicates severe leaf necrosislesions, whereas a score of 9 indicates no lesions. Preliminary scoresare reported as double digits, for example ‘55’ indicates a preliminaryscore of 5 on the scale of 1 to 9.

FLOWER COLOR. Data values include: P=purple and W=white.

GENE SILENCING. The interruption or suppression of the expression of anucleic acid sequence at the level of transcription or translation.

GENOTYPE. Refers to the genetic constitution of a cell or organism.

PLANT HABIT. This refers to the physical appearance of a plant. It canbe determinate (Det), semi-determinate, intermediate, or indeterminate(Ind). In soybeans, indeterminate varieties are those in which stemgrowth is not limited by formation of a reproductive structure (i.e.,flowers, pods and seeds) and hence growth continues throughout floweringand during part of pod filling. The main stem will develop and set podsover a prolonged period under favorable conditions. In soybeans,determinate varieties are those in which stem growth ceases at floweringtime. Most flowers develop simultaneously, and most pods fill atapproximately the same time. The terms semi-determinate and intermediateare also used to describe plant habit and are defined in Bernard, R. L.(1972) “Two genes affecting stem termination in soybeans.” Crop Science12:235-239; Woodworth, C. M. (1932) “Genetics and breeding in theimprovement of the soybean.” Bull. Agric. Exp. Stn. (Illinois)384:297-404; and Woodworth, C. M. (1933) “Genetics of the Soybean.” J.Am. Soc. Agron. 25:36-51.

HAPLOID. A cell or organism having one set of the two sets ofchromosomes in a diploid cell or organism.

HERBRES=Herbicide Resistance. This indicates that the plant is moretolerant to the herbicide shown than the level of herbicide toleranceexhibited by wild type plants. A designation of ‘Gly’ indicatestolerance to glyphosate, and a designation of ‘STS’ indicates toleranceto sulfonylurea herbicides.

HGT=Plant Height. Plant height is taken from the top of the soil to thetop pod of the plant and is measured in inches.

HILUM. This refers to the scar left on the seed which marks the placewhere the seed was attached to the pod prior to harvest. Hila Color datavalues include: BR=brown; TN=tan; Y=yellow; BL=black; IB=ImperfectBlack; BF=buff. Tan hila may also be designated as imperfect yellow(IY).

HLC=HO=High Oleic. Oil with seventy percent or more oleic acid isclassified as high oleic oil. Oleic acid is one of the five mostabundant fatty acids in soybean seeds. It is measured by gaschromatography and is reported as a percent of the total oil content.

HYPLSC=Hypocotyl length=Hypocotyl elongation. This score indicates theability of the seed to emerge when planted 3″ deep in sand pots and witha controlled temperature of 25° C. The number of plants that emerge eachday are counted. Based on this data, each genotype is given a score from1 to 9 based on its rate of emergence and the percent of emergence. Ascore of 1 indicates a very poor rate and percent of emergence, anintermediate score of 5 indicates average ratings, and a score of 9indicates an excellent rate and percent of emergence. Preliminary scoresare reported as double digits, for example ‘55’ indicates a preliminaryscore of 5 on the scale of 1 to 9.

HYPOCOTYL. A hypocotyl is the portion of an embryo or seedling betweenthe cotyledons and the root.

LDGSEV=Lodging Resistance=Harvest Standability. Lodging is rated on ascale of 1 to 9. A score of 1 indicates plants that are lying on theground, a score of 5 indicates plants are leaning at a 45° angle inrelation to the ground, and a score of 9 indicates erect plants.Preliminary scores are reported as double digits, for example ‘55’indicates a preliminary score of 5 on the scale of 1 to 9.

LEAFLETS. These are parts of the plant shoot involved in the manufactureof food for the plant by the process of photosynthesis.

LINKAGE. Refers to a phenomenon wherein alleles on the same chromosometend to segregate together more often than expected by chance if theirtransmission was independent.

LINKAGE DISEQUILIBRIUM. Refers to a phenomenon wherein alleles tend toremain together in linkage groups when segregating from parents tooffspring, with a greater frequency than expected from their individualfrequencies.

LLC=Oil with three percent or less linolenic acid is classified as lowlinolenic oil. Linolenic acid is one of the five most abundant fattyacids in soybean seeds. It is measured by gas chromatography and isreported as a percent of the total oil content.

LLE=Linoleic Acid Percent. Linoleic acid is one of the five mostabundant fatty acids in soybean seeds. It is measured by gaschromatography and is reported as a percent of the total oil content.

LLN=Linolenic Acid Percent. Linolenic acid is one of the five mostabundant fatty acids in soybean seeds. It is measured by gaschromatography and is reported as a percent of the total oil content.

LOCUS. A defined segment of DNA.

LOCUS CONVERSION. Refers to seeds, plants, and/or parts thereofdeveloped by backcrossing wherein essentially all of the desiredmorphological and physiological characteristics of a variety arerecovered in addition to at least one locus which has been transferredinto the variety. The locus can be a native locus, a transgenic locus,or a combination thereof.

PRM=PRMMAT=Predicted Relative Maturity=RM=Relative Maturity. Soybeanmaturities are divided into relative maturity groups (denoted as 000,00, 0, I, II, III, IV, V, VI, VII, VIII, IX, X, or 000, 00, 0, 1, 2, 3,4, 5, 6, 7, 8, 9, 10). Within a maturity group are sub-groups. Asub-group is a tenth of a relative maturity group (for example 1.3 wouldindicate a group 1 and subgroup 3). Within narrow comparisons, thedifference of a tenth of a relative maturity group equates very roughlyto a day difference in maturity at harvest.

MAT ABS=ABSOLUTE MATURITY. This term is defined as the length of timefrom planting to complete physiological development (maturity). Theperiod from planting until maturity is reached is measured in days,usually in comparison to one or more standard varieties. Plants areconsidered mature when 95% of the pods have reached their mature color.

MATURITY GROUP. This refers to an agreed-on industry division of groupsof varieties, based on the zones in which they are adapted primarilyaccording to day length or latitude. They consist of very long daylength varieties (Groups 000, 00, 0), and extend to very short daylength varieties (Groups VII, VIII, IX, X).

NARROW ROWS. Term indicates 7″ and 15″ row spacing.

NEI DISTANCE. A quantitative measure of percent similarity between twolines. Nei's distance between lines A and B can be defined as1−((2*number alleles in common)/(number alleles in A+number alleles inB)). For example, if lines A and B are the same for 95 out of 100alleles, the Nei distance would be 0.05. If lines A and B are the samefor 98 out of 100 alleles, the Nei distance would be 0.02. Free softwarefor calculating Nei distance is available on the internet at multiplelocations such as, e.g., evolution.genetics.washington.edu/phylip.html.See Nei & Li (1979) Proc Natl Acad Sci USA 76:5269-5273, which isincorporated by reference for this purpose.

NUCLEIC ACID. An acidic, chain-like biological macromolecule consistingof multiple repeat units of phosphoric acid, sugar, and purine andpyrimidine bases.

OIL=OIL PERCENT=OIL (%). Soybean seeds contain a considerable amount ofoil. Oil is measured by NIR spectrophotometry and is reported as apercentage basis.

OIL/MEAL TYPE. Designates varieties specially developed with thefollowing oil traits: HLC=High Oleic oil (>70% oleic contect); LLC=LowLinolenic (<3% linolenic content); ULC=Ultra Low Linolenic oil (<1%linolenic oil content).

OLC=OLEIC ACID PERCENT. Oleic acid is one of the five most abundantfatty acids in soybean seeds. It is measured by gas chromatography andis reported as a percent of the total oil content.

PEDIGREE DISTANCE. Relationship among generations based on theirancestral links as evidenced in pedigrees. May be measured by thedistance of the pedigree from a given starting point in the ancestry.

PERCENT IDENTITY. Percent identity as used herein refers to thecomparison of the homozygous alleles of two soybean varieties. Percentidentity is determined by comparing a statistically significant numberof the homozygous alleles of two developed varieties. For example, apercent identity of 90% between soybean variety 1 and soybean variety 2means that the two varieties have the same allele at 90% of the lociused in the comparison.

PERCENT SIMILARITY. Percent similarity as used herein refers to thecomparison of the homozygous alleles of a soybean variety such asXB39AE12 with another plant, and if the homozygous allele of XB39AE12matches at least one of the alleles from the other plant, then they arescored as similar. Percent similarity is determined by comparing astatistically significant number of loci and recording the number ofloci with similar alleles as a percentage. A percent similarity of 90%between XB39AE12 and another plant means that XB39AE12 matches at leastone of the alleles of the other plant at 90% of the loci used in thecomparison.

PLANT. As used herein, the term “plant” includes reference to animmature or mature whole plant, including a plant from which seed orgrain or anthers have been removed. Any seed or embryo that will producethe plant is also considered to be the plant.

PLANT PARTS. As used herein, the term “plant parts” includes leaves,stems, roots, root tips, anthers, seed, grain, embryos, pollen, ovules,flowers, cotyledon, hypocotyl, pod, flower, shoot, stalk, tissue, tissuecultures, cells and the like.

PLM or PALMITIC ACID PERCENT. Palmitic acid is one of the five mostabundant fatty acids in soybean seeds. It is measured by gaschromatography and is reported as a percent of the total oil content.

PMG infested soils. Soils containing Phytophthora sojae.

POD. This refers to the fruit of a soybean plant. It consists of thehull or shell (pericarp) and the soybean seeds. Pod Color data valuesinclude: BR=brown; TN=tan.

POWDERY MILDEW. Powdery Mildew is caused by a fungus, Microsphaeradiffuse. Tolerance to Powdery Mildew is rated on a scale of 1 to 9, witha score of 1 being very susceptible ranging up to a score of 9 beingtolerant. Preliminary scores are reported as double digits, for example‘55’ indicates a preliminary score of 5 on the scale of 1 to 9.

PRT or PHYTOPHTHORA FIELD TOLERANCE. Tolerance to Phytophthora root rotis rated on a scale of 1 to 9, with a score of 1 indicating the plantshave no tolerance to Phytophthora, ranging to a score of 9 being thebest or highest tolerance. PRTLAB indicates the tolerance was scoredusing plants in lab assay experiments. Preliminary scores are reportedas double digits, for example ‘55’ indicates a preliminary score of 5 onthe scale of 1 to 9.

PHYTOPHTHORA RESISTANCE GENE (Rps). Various Phytophthora resistancegenes are known and include but are not limited to: Rps1-a=resistance toraces 1-2, 10-11, 13-8, 24; Rps1-c=resistance to races 1-3, 6-11, 13,15, 17, 21, 23, 24, 26, 28-30, 32, 34, 36; Rps1-k=resistance to races1-11, 13-15, 17, 18, 21-24, 26, 36, 37; Rps3-a=resistance to races 1-5,8, 9, 11, 13, 14, 16, 18, 23, 25, 28, 29, 31-35, 39-41, 43-45, 47-52,54; Rps3-c=resistance to races 1-4, 10-16, 18-36, 38-54; Rps6=resistanceto races 1-4, 10, 12, 14-16, 18-21, 25, 28, 33-35; and, Rps8=resistanceto races 1-5, 9, 13-15, 21, 25, 29, 32. As reported in Table 1 “-” or “” indicates that a specific gene for resistance has not been identifiedto date.

PRO=PROTN=PROTN (%)=PROTEIN PERCENT. Soybean seeds contain aconsiderable amount of protein. Protein is generally measured by NIRspectrophotometry, and is reported as a percent on a dry weight basis.

PUBESCENCE. This refers to a covering of very fine hairs closelyarranged on the leaves, stems and pods of the soybean plant. Pubescencecolor data values include: L=Light Tawny; T=Tawny; G=Gray.

R160=Palmitic Acid percentage. Percentage of palmitic acid as determinedusing methods described in Reske et al. (1997) “TriacylglycerolComposition and Structure in Genetically Modified Sunflower and SoybeanOils” JAOCS 74:989-998, which is incorporated by reference for thispurpose.

R180=Stearic acid percentage. Percentage of Stearic acid as determinedusing methods described in Reske et al. (1997) JAOCS 74:989-998, whichis incorporated by reference for this purpose.

R181=Oleic acid percentage. Percentage of oleic acid as determined usingmethods described in Reske et al. (1997) JAOCS 74:989-998, which isincorporated by reference for this purpose.

R182=Linoleic acid percentage. Percentage of linoleic acid as determinedusing methods described in Reske et al. (1997) JAOCS 74:989-998, whichis incorporated by reference for this purpose.

R183=Linolenic acid percentage. Percentage of linolenic acid asdetermined using methods described in Reske et al. (1997) JAOCS74:989-998, which is incorporated by reference for this purpose.

RESISTANCE. As used herein, resistance is synonymous with tolerance andis used to describe the ability of a plant to withstand exposure to aninsect, disease, herbicide, environmental stress, or other condition. Aresistant plant variety will be able to better withstand the insect,disease pathogen, herbicide, environmental stress, or other condition ascompared to a non-resistant or wild-type variety.

RKI=SOUTHERN ROOT-KNOT NEMATODE. Southern root knot nematode,Meloidogyne incognita, is a plant parasite that can cause major damageto roots, reducing yield potential. Severity is visually scored on rootsin a range from 1 to 9 comparing all genotypes in a given experiment toknown resistant and susceptible checks. The score is determined byvisually scoring the roots for presence or absence of galling in acontrolled chamber bioassay. A score of 1 indicates severe galling ofthe root system which can cause premature death from decomposition ofthe root system (susceptible). A score of 9 indicates that there islittle to no galling of the roots (resistant). Preliminary scores arereported as double digits, for example ‘55’ indicates a preliminaryscore of 5 on the scale of 1 to 9.

RKA=PEANUT ROOT-KNOT NEMATODE. Peanut root knot nematode, Meloidogynearenaria, is a plant parasite that can cause major damage to roots,reducing yield potential. Severity is visually scored on roots in arange from 1 to 9 comparing all genotypes in a given experiment to knownresistant and susceptible checks. The score is determined by visuallyscoring the roots for presence or absence of galling in a controlledchamber bioassay. A score of 1 indicates severe galling of the rootsystem which can cause pre-mature death from decomposition of the rootsystem (susceptible). A score of 9 indicates that there is little to nogalling of the roots (resistant). Preliminary scores are reported asdouble digits, for example ‘55’ indicates a preliminary score of 5 onthe scale of 1 to 9.

RKJ=JAVANICA ROOT-KNOT NEMATODE. Javonica root knot nematode,Meloidogyne javonica, is a plant parasite that can cause major damage toroots, reducing yield potential. Severity is visually scored on roots ina range from 1 to 9 comparing all genotypes in a given experiment toknown resistant and susceptible checks. The score is determined byvisually scoring the roots for presence or absence of galling in acontrolled chamber bioassay. A score of 1 indicates severe galling ofthe root system which can cause premature death from decomposition ofthe root system (susceptible). A score of 9 indicates that there islittle to no galling of the roots (resistant). Preliminary scores arereported as double digits, for example ‘55’ indicates a preliminaryscore of 5 on the scale of 1 to 9.

SCN=SOYBEAN CYST NEMATODE RESISTANCE=Cyst Nematode Resistance. The scoreis based on resistance to a particular race of soybean cyst nematode(Heterodera glycines), such as race 1, 2, 3, 5 or 14. Scores are from 1to 9 and indicate visual observations of resistance as compared to othergenotypes in the test. A score of 1 indicates nematodes are able toinfect the plant and cause yield loss, while a score of 9 indicates SCNresistance. Preliminary scores are reported as double digits, forexample ‘55’ indicates a preliminary score of 5 on the scale of 1 to 9.

SCN Resistance Source. There are three typical sources of geneticresistance to SCN: PI88788, PI548402 (also known as Peking), andPI437654 (also known as Hartwig).

SCN infected soils. Soils containing soybean cyst nematode.

SD VIG or Seedling Vigor. The score is based on the speed of emergenceof the plants within a plot relative to other plots within anexperiment. A score of 1 indicates no plants have expanded first leaves,while a score of 9 indicates that 90% of plants growing have expandedfirst leaves.

SDS or SUDDEN DEATH SYNDROME. SDS is caused by the fungal pathogenformerly known as Fusarium solani fsp. glycines, which is currentlyknown as Fusarium virguliforme (see, e.g., Aoki et al. (2003) Mycologia95:660-684). Tolerance to Sudden Death Syndrome is rated on a scale of 1to 9, with a score of 1 being very susceptible ranging up to a score of9 being tolerant. Preliminary scores are reported as double digits, forexample ‘55’ indicates a preliminary score of 5 on the scale of 1 to 9.

SEED COAT LUSTER. Data values include D=dull; S=shiny.

SEED SIZE SCORE. This is a measure of the seed size from 1 to 9. Thehigher the score, the smaller the seed size measured. Preliminary scoresare reported as double digits, for example ‘55’ indicates a preliminaryscore of 5 on the scale of 1 to 9.

SEPTORIA LEAF SPOT. Septoria Leaf Spot, also known as Brown Spot, iscaused by the fungus Septoria glycines. Symptoms can occur as early asV2 on lower leaves, and may move up the plant affecting leaves as wellas stems and pods in plants approaching maturity. Symptoms includeirregular dark brown spots on upper and lower leaf surfaces, or thestems or pods. Infected leaves may yellow or brown and drop early.Tolerance to Septoria Leaf Spot is rated on a scale of 1 to 9, with ascore of 1 being very susceptible ranging up to a score of 9 beingtolerant. Preliminary scores are reported as double digits, for example‘55’ indicates a preliminary score of 5 on the scale of 1 to 9.

SPLB=S/LB=Seeds per Pound. Soybean seeds vary in seed size, therefore,the number of seeds required to make up one pound also varies. Thisaffects the pounds of seed required to plant a given area, and can alsoimpact end uses.

SHATTR or Shattering. This refers to the amount of pod dehiscence priorto harvest. Pod dehiscence involves seeds falling from the pods to thesoil. This is a visual score from 1 to 9 comparing all genotypes withina given test. A score of 1 indicates 100% of the pods are opened, whilea score of 9 means pods have not opened and no seeds have fallen out.

SHOOTS. These are a portion of the body of the plant. They consist ofstems, petioles and leaves.

STC or Stearic Acid Percent. Stearic acid is one of the five mostabundant fatty acids in soybean seeds. It is measured by gaschromatography and is reported as a percent of the total oil content.

SUBLINE. Although XB39AE12 contains substantially fixed genetics, and isphenotypically uniform and with no off-types expected, there stillremains a small proportion of segregating loci either within individualsor within the population as a whole. The segregating loci both withinany individual plant and/or the population can be used to extract uniquevarieties (sublines) with similar phenotype but improved agronomics.

TARGET SPOT. This is a fungal disease caused by Corynespora cassiicola.Symptoms usually consist of roughly circular, necrotic leaf lesions fromminute to 11 mm in diameter, though typically approximately 4 to 5 mm indiameter, and with a yellow margin. Large lesions occasionally exhibit azonate pattern associated with this disease. Tolerance to target spot isscored from 1 to 9 by visually comparing all genotypes in a given test.A score of 1 indicates complete death of the experimental unit while ascore of 9 indicates no symptoms. Preliminary scores are reported asdouble digits, for example ‘55’ indicates a preliminary score of 5 onthe scale of 1 to 9.

WHMD or WHITE MOLD TOLERANCE. This is a fungal disease caused bySclerotinia sclerotiorum that creates mycelial growth and death ofplants. Tolerance to white mold is scored from 1 to 9 by visuallycomparing all genotypes in a given test. A score of 1 indicates completedeath of the experimental unit while a score of 9 indicates no symptoms.Preliminary scores are reported as double digits, for example ‘55’indicates a preliminary score of 5 on the scale of 1 to 9.

VARIETY. A substantially homozygous soybean line and minor modificationsthereof that retains the overall genetics of the soybean line includingbut not limited to a subline, a locus conversion, a mutation, atransgenic, or a somaclonal variant. Variety includes seeds, plants,plant parts, and/or seed parts of the instant soybean line.

HIGH YIELD ENVIRONMENTS. Areas which lack normal stress, typicallyhaving sufficient rainfall, water drainage, low disease pressure, andlow weed pressure.

TOUGH ENVIRONMENTS. Areas which have stress challenges, opposite of ahigh yield environment.

DETAILED DESCRIPTION

Soybean variety XB39AE12 has shown uniformity and stability for alltraits, as described in the following variety description information.Soybean variety XB39AE12 was developed from a cross of 93M61 with 94Y01.Variety XB39AE12 is an F3-derived line which was advanced to the F3generation by modified single-seed descent. It has been self-pollinateda sufficient number of generations, with careful attention to uniformityof plant type to ensure a sufficient level of homozygosity andphenotypic stability. The variety has been increased with continuedobservation for uniformity. No variant traits have been observed or areexpected.

A variety description of soybean variety XB39AE12 is provided inTable 1. Traits reported are average values for all locations and yearsor samples measured. Preliminary scores are reported as double digits,for example ‘55’ indicates a preliminary score of 5 on the scale of 1 to9.

Soybean variety XB39AE12, being substantially homozygous, can bereproduced by planting seeds of the variety, growing the resultingsoybean plants under self-pollinating or sib-pollinating conditions, andharvesting the resulting seed, using techniques familiar to theagricultural arts. Development of soybean variety XB39AE12 is shown inthe breeding history summary in Table 4.

Performance Examples of XB39AE12

As shown in Table 2, the traits and characteristics of soybean varietyXB39AE12 are given in paired comparisons with other varieties. Traitsreported are mean values for all locations and years where pairedcomparison data was obtained.

Genetic Marker Profile

In addition to phenotypic observations, a plant can also be identifiedby its genotype. The genotype of a plant can be characterized through agenetic marker profile which can identify plants of the same variety ora related variety, or which can be used to determine or validate apedigree. Genetic marker profiles can be obtained by techniques such asrestriction fragment length polymorphisms (RFLPs), randomly amplifiedpolymorphic DNAs (RAPDs), arbitrarily primed polymerase chain reaction(AP-PCR), DNA amplification fingerprinting (DAF), sequence characterizedamplified regions (SCARs), amplified fragment length polymorphisms(AFLPs), simple sequence repeats (SSRs) also referred to asmicrosatellites, or single nucleotide polymorphisms (SNPs). For example,see Cregan et al. (1999) “An Integrated Genetic Linkage Map of theSoybean Genome” Crop Science 39:1464-1490, and Berry et al. (2003)“Assessing Probability of Ancestry Using Simple Sequence RepeatProfiles: Applications to Maize Inbred Lines and Soybean Varieties”Genetics 165:331-342, each of which are incorporated by reference hereinin their entirety.

Methods of characterizing soybean variety XB39AE12, or a varietycomprising the morphological and physiological characteristics ofsoybean variety XB39AE12, are provided. In one example a methodcomprising isolating nucleic acids from a plant, a plant part, or a seedof soybean variety XB39AE12, analyzing said nucleic acids to producedata, and recording the data for XB39AE12 is provided. In some examplesthe data comprises one of more of a nucleic acid sequence, a geneticprofile, a molecular profile, a marker profile, a haplotype, or anycombination thereof. In some examples, the data is recorded on acomputer readable medium. In other examples, the methods may furthercomprise using the data for soybean crossing, selection and/oradvancement decisions. Crossing includes any type of plant breedingcrossing method, including but not limited to outcrossing, selfing,backcrossing, locus conversion, introgression and the like.

In some examples, one or more markers are used to characterize and/orevaluate a soybean variety. Particular markers used for these purposesare not limited to any particular set of markers, but are envisioned toinclude any type of marker and marker profile which provides a means ofdistinguishing varieties. For example, one set of publicly availablemarkers which could be used to screen and identify variety XB39AE12 isdisclosed in Table 3. In another example, one method of comparison is touse only homozygous loci for XB39AE12.

Primers and PCR protocols for assaying these and other markers aredisclosed in Soybase (sponsored by the USDA Agricultural ResearchService and Iowa State University) located on the world wide web at129.186.26.94/SSR.html. In addition to being used for identification ofsoybean variety XB39AE12, and plant parts and plant cells of varietyXB39AE12, the genetic profile may be used to identify a soybean plantproduced through the use of XB39AE12 or to verify a pedigree for progenyplants produced through the use of XB39AE12. The genetic marker profileis also useful in breeding and developing backcross conversions.

The present invention comprises a soybean plant characterized bymolecular and physiological data obtained from the representative sampleof said variety deposited with the American Type Culture Collection(ATCC). Thus, plants, seeds, or parts thereof, having all orsubstantially all of the physiological and morphological characteristicsof soybean variety XB39AE12 are provided. Further provided is a soybeanplant formed by the combination of the disclosed soybean plant or plantcell with another soybean plant or cell and comprising the homozygousalleles of the variety. A soybean plant comprising all of thephysiological and morphological characteristics of soybean varietyXB39AE12 can be combined with another soybean plant in a soybeanbreeding program. In some examples the other soybean plant comprises allof the physiological and morphological characteristics of soybeanvariety XB39AE12.

In some examples, a plant, a plant part, or a seed of soybean varietyXB39AE12 is characterized by producing a molecular profile. A molecularprofile includes but is not limited to one or more genotypic and/orphenotypic profile(s). A genotypic profile includes but is not limitedto a marker profile, such as a genetic map, a linkage map, a traitmarker profile, a SNP profile, an SSR profile, a genome-wide markerprofile, a haplotype, and the like. A molecular profile may also be anucleic acid sequence profile, and/or a physical map. A phenotypicprofile includes but is not limited to a protein expression profile, ametabolic profile, an mRNA expression profile, and the like.

Means of performing genetic marker profiles using SSR polymorphisms arewell known in the art. A marker system based on SSRs can be highlyinformative in linkage analysis relative to other marker systems in thatmultiple alleles may be present. Another advantage of this type ofmarker is that, through use of flanking primers, detection of SSRs canbe achieved, for example, by using the polymerase chain reaction (PCR),thereby eliminating the need for labor-intensive Southern hybridization.PCR detection is done using two oligonucleotide primers flanking thepolymorphic segment of repetitive DNA to amplify the SSR region.

Following amplification, markers can be scored by electrophoresis of theamplification products. Scoring of marker genotype is based on the sizeof the amplified fragment, which correlates to the number of base pairsof the fragment. While variation in the primer used or in laboratoryprocedures can affect the reported fragment size, relative values shouldremain constant regardless of the specific primer or laboratory used.When comparing varieties it is preferable if all SSR profiles areperformed in the same lab.

Primers used are publicly available and may be found in Soybase orCregan (1999 Crop Science 39:1464-1490). See also, WO 99/31964“Nucleotide Polymorphisms in Soybean”, U.S. Pat. No. 6,162,967“Positional Cloning of Soybean Cyst Nematode Resistance Genes”, and U.S.Pat. No. 7,288,386 “Soybean Sudden Death Syndrome Resistant Soybeans andMethods of Breeding and Identifying Resistant Plants”, the disclosuresof which are incorporated herein by reference.

The SSR profile of soybean plant XB39AE12 can be used to identify plantscomprising XB39AE12 as a parent, since such plants will comprise thesame homozygous alleles as XB39AE12. Because the soybean variety isessentially homozygous at all relevant loci, most loci should have onlyone type of allele present. In contrast, a genetic marker profile of anF1 progeny should be the sum of those parents, e.g., if one parent washomozygous for allele X at a particular locus, and the other parenthomozygous for allele Y at that locus, then the F1 progeny will be XY(heterozygous) at that locus. Subsequent generations of progeny producedby selection and breeding are expected to be of genotype XX(homozygous), YY (homozygous), or XY (heterozygous) for that locusposition. When the F1 plant is selfed or sibbed for successive filialgenerations, the locus should be either X or Y for that position.

In addition, plants and plant parts substantially benefiting from theuse of XB39AE12 in their development, such as XB39AE12 comprising abackcross conversion, transgene, or genetic sterility factor, may beidentified by having a molecular marker profile with a high percentidentity to XB39AE12. Such a percent identity might be 90%, 91%, 92%,93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5%, or 99.9% identical toXB39AE12.

The SSR profile of variety XB39AE12 also can be used to identifyessentially derived varieties and other progeny varieties developed fromthe use of XB39AE12, as well as cells and other plant parts thereof.Plants of the invention include any plant having at least 90%, 91%, 92%,93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5%, or 99.9% of the markers in theSSR profile, and that retain 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%,98%, 99%, 99.5%, or 99.9% of the physiological and morphologicalcharacteristics of variety XB39AE12 when grown under the sameconditions. Such plants may be developed using the markers identified inWO 00/31964, U.S. Pat. No. 6,162,967 and U.S. Pat. No. 7,288,386.Progeny plants and plant parts produced using XB39AE12 may be identifiedby having a molecular marker profile of at least 25%, 30%, 35%, 40%,45%, 50%, 55%, 60%, 65%, 70%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%,83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%,97%, 98%, 99% or 99.5% genetic contribution from soybean varietyXB39AE12, as measured by either percent identity or percent similarity.Such progeny may be further characterized as being within a pedigreedistance of XB39AE12, such as within 1, 2, 3, 4, or 5 or lesscross-pollinations to a soybean plant other than XB39AE12, or a plantthat has XB39AE12 as a progenitor. Unique molecular profiles may beidentified with other molecular tools such as SNPs and RFLPs.

Introduction of a New Trait or Locus into XB39AE12

Variety XB39AE12 represents a new base genetic variety into which a newlocus or trait may be introgressed. Direct transformation andbackcrossing represent two important methods that can be used toaccomplish such an introgression.

A backcross conversion of XB39AE12 occurs when DNA sequences areintroduced through backcrossing (Hallauer et al. in Corn and CornImprovement, Sprague and Dudley, Third Ed. 1998) with XB39AE12 utilizedas the recurrent parent. Both naturally occurring and transgenic DNAsequences may be introduced through backcrossing techniques. A backcrossconversion may produce a plant with a trait or locus conversion in atleast two or more backcrosses, including at least 2 backcrosses, atleast 3 backcrosses, at least 4 backcrosses, at least 5 backcrosses, ormore. Molecular marker assisted breeding or selection may be utilized toreduce the number of backcrosses necessary to achieve the backcrossconversion. For example, see Openshaw et al., “Marker-assisted Selectionin Backcross Breeding”. In: Proceedings Symposium of the Analysis ofMolecular Data, August 1994, Crop Science Society of America, Corvallis,Oreg., which demonstrated that a backcross conversion can be made in asfew as two backcrosses.

The complexity of the backcross conversion method depends on the type oftrait being transferred (a single gene or closely linked genes comparedto unlinked genes), the level of expression of the trait, the type ofinheritance (cytoplasmic or nuclear), dominant or recessive traitexpression, and the types of parents included in the cross. It isunderstood by those of ordinary skill in the art that for single genetraits that are relatively easy to classify, the backcross method iseffective and relatively easy to manage. (See Hallauer et al., in Cornand Corn Improvement, Sprague and Dudley, Third Ed. 1998). Desiredtraits that may be transferred through backcross conversion include, butare not limited to, sterility (nuclear and cytoplasmic), fertilityrestoration, nutritional enhancements, drought tolerance, nitrogenutilization, altered fatty acid profile, low phytate, industrialenhancements, disease resistance (bacterial, fungal, or viral), insectresistance, and herbicide resistance. In addition, a recombination siteitself, such as an FRT site, Lox site, or other site specificintegration site, may be inserted by backcrossing and utilized fordirect insertion of one or more genes of interest into a specific plantvariety. A single locus may contain several transgenes, such as atransgene for disease resistance and a transgene for herbicideresistance. The gene for herbicide resistance may be used as aselectable marker and/or as a phenotypic trait. A single locusconversion of site specific integration system allows for theintegration of multiple genes at a known recombination site in thegenome.

The backcross conversion may result from either the transfer of adominant allele or a recessive allele. Selection of progeny containingthe trait of interest can be accomplished by direct selection for atrait associated with a dominant allele. Transgenes transferred viabackcrossing typically function as a dominant single gene trait and arerelatively easy to classify. Selection of progeny for a trait that istransferred via a recessive allele requires growing and selfing thefirst backcross generation to determine which plants carry the recessivealleles. Recessive traits may require additional progeny testing insuccessive backcross generations to determine the presence of the locusof interest. The last backcross generation is usually selfed to givepure breeding progeny for the trait(s) being transferred, although abackcross conversion with a stably introgressed trait may also bemaintained by further backcrossing to the recurrent parent withsubsequent selection for the trait.

Along with selection for the trait of interest, progeny are selected forthe phenotype of the recurrent parent. The backcross is a form ofinbreeding, and the features of the recurrent parent are automaticallyrecovered after successive backcrosses. Poehlman suggests from one tofour or more backcrosses, but as noted above, the number of backcrossesnecessary can be reduced with the use of molecular markers (Poehlman etal., (1995) Breeding Field Crops, 4th Ed., Iowa State University Press,Ames, Iowa). Other factors, such as a genetically similar donor parent,may also reduce the number of backcrosses necessary. As noted byPoehlman, backcrossing is easiest for simply inherited, dominant, andeasily recognized traits.

One process for adding or modifying a trait or locus in soybean varietyXB39AE12 comprises crossing XB39AE12 plants grown from XB39AE12 seedwith plants of another soybean plant that comprises a desired traitlacking in XB39AE12, selecting F1 progeny plants that possess thedesired trait or locus to produce selected F1 progeny plants, crossingthe selected progeny plants back to XB39AE12 plants to producebackcross1 (BC1) progeny plants. The BC1F1 progeny plants that have thedesired trait and the morphological characteristics of soybean varietyXB39AE12 are selected and backcrossed to XB39AE12 to generate BC2F1progeny plants. Additional backcrossing and selection of progeny plantswith the desired trait will produce BC3F1, BC4F1, BC5F1, . . . BCxF1generations of plants. The backcross populations of XB39AE12 may befurther characterized as having the physiological and morphologicalcharacteristics of soybean variety XB39AE12 listed in Table 1 asdetermined at the 5% significance level when grown in the sameenvironmental conditions and/or may be characterized by percentsimilarity or identity to XB39AE12 as determined by SSR or othermolecular markers. The above method may be utilized with fewerbackcrosses in appropriate situations, such as when the donor parent ishighly related or molecular markers are used in one or more selectionsteps. Desired traits that may be used include those nucleic acids knownin the art, some of which are listed herein, that will affect traitsthrough nucleic acid expression or inhibition. Desired loci also includethe introgression of FRT, Lox, and/or other recombination sites for sitespecific integration. Desired loci further include QTLs, which may alsoaffect a desired trait.

In addition, the above process and other similar processes describedherein may be used to produce first generation progeny soybean seed byadding a step at the end of the process that comprises crossing XB39AE12with the introgressed trait or locus with a different soybean plant andharvesting the resultant first generation progeny soybean seed.

Transgenes and transformation methods provide means to engineer thegenome of plants to contain and express heterologous genetic elements,including but not limited to foreign genetic elements, additional copiesof endogenous elements, and/or modified versions of native or endogenousgenetic elements, in order to alter at least one trait of a plant in aspecific manner that would be difficult or impossible to obtain withtraditional plant breeding alone. Any heterologous DNA sequence(s),whether from a different species or from the same species, which areinserted into the genome using transformation, backcrossing, or othermethods known to one of skill in the art are referred to hereincollectively as transgenes. The sequences are heterologous based onsequence source, location of integration, operably linked elements, orany combination thereof. One or more transgenes of interest can beintroduced into soybean variety XB39AE12. Transgenic variants of soybeanvariety XB39AE12 plants, seeds, cells, and parts thereof or derivedtherefrom are provided. Transgenic variants of XB39AE12 comprise thephysiological and morphological characteristics of soybean varietyXB39AE12 listed in Table 1 as determined at the 5% significance levelwhen grown in the same environmental conditions, and/or may becharacterized or identified by percent similarity or identity toXB39AE12 as determined by SSR or other molecular markers. In someexamples, transgenic variants of soybean variety XB39AE12 are producedby introducing at least one transgene of interest into soybean varietyXB39AE12 by transforming XB39AE12 with a polynucleotide comprising thetransgene of interest. In other examples, transgenic variants of soybeanvariety XB39AE12 are produced by introducing at least one transgene byintrogressing the transgene into soybean variety XB39AE12 by crossing.

In one example, a process for modifying soybean variety XB39AE12 withthe addition of a desired trait, said process comprising transforming asoybean plant of variety XB39AE12 with a transgene that confers adesired trait is provided. Therefore, transgenic XB39AE12 soybean cells,plants, plant parts, and seeds produced from this process are provided.In some examples one more desired traits may include traits such asherbicide resistance, insect resistance, disease resistance, decreasedphytate, modified fatty acid profile, modified fatty acid content,carbohydrate metabolism, protein content, or oil content. The specificgene may be any known in the art or listed herein, including but notlimited to a polynucleotide conferring resistance to imidazolinone,sulfonylurea, protoporphyrinogen oxidase (PPO) inhibitors, hydroxyphenylpyruvate dioxygenase (HPPD) inhibitors, glyphosate, glufosinate,triazine, 2,4-dichlorophenoxyacetic acid (2,4-D), dicamba, broxynil,metribuzin, or benzonitrile herbicides; a polynucleotide encoding aBacillus thuringiensis polypeptide, a polynucleotide encoding a phytase,a fatty acid desaturase (e.g., FAD-2, FAD-3), galactinol synthase, araffinose synthetic enzyme; or a polynucleotide conferring resistance tosoybean cyst nematode, brown stem rot, Phytophthora root rot, soybeanmosaic virus, sudden death syndrome, or other plant pathogen.

Numerous methods for plant transformation have been developed, includingbiological and physical plant transformation protocols. See, forexample, Miki et al., “Procedures for Introducing Foreign DNA intoPlants” in Methods in Plant Molecular Biology and Biotechnology, Glick,B. R. and Thompson, J. E. Eds. (CRC Press, Inc., Boca Raton, 1993) pages67-88; and Armstrong (1999) “The First Decade of Maize Transformation: AReview and Future Perspective” Maydica 44:101-109. In addition,expression vectors and in vitro culture methods for plant cell or tissuetransformation and regeneration of plants are available. See, forexample, Gruber et al., “Vectors for Plant Transformation” in Methods inPlant Molecular Biology and Biotechnology, Glick, B. R. and Thompson, J.E. Eds. (CRC Press, Inc., Boca Raton, 1993) pages 89-119.

The most prevalent types of plant transformation methods involve theconstruction of an expression vector. Such a vector comprises a DNAsequence that contains a gene under the control of or operatively linkedto a regulatory element, for example a promoter. The vector may containone or more genes and one or more regulatory elements.

A genetic trait which has been engineered into the genome of aparticular soybean plant may then be moved into the genome of anothervariety using traditional breeding techniques that are well known in theplant breeding arts. For example, a backcrossing approach is commonlyused to move a transgene from a transformed soybean variety into anelite soybean variety, and the resulting backcross conversion plantwould then contain the transgene(s).

Various genetic elements can be introduced into the plant genome usingtransformation. These elements include, but are not limited to genes;coding sequences; inducible, constitutive, and tissue specificpromoters; enhancing sequences; and signal and targeting sequences.

Transgenic plants can be used to produce commercial quantities of aforeign protein. Thus, techniques for the selection and propagation oftransformed plants, which are well understood in the art, yield aplurality of transgenic plants that are harvested in a conventionalmanner, and a heterologous protein then can be extracted from a tissueof interest or from total biomass. Protein extraction from plant biomasscan be accomplished by known methods which are discussed, for example,by Heney and Orr (1981) Anal. Biochem. 114:92-6.

A genetic map can be generated that identifies the approximatechromosomal location of the integrated DNA molecule, for example viaconventional restriction fragment length polymorphisms (RFLP),polymerase chain reaction (PCR) analysis, simple sequence repeats (SSR),and single nucleotide polymorphisms (SNP). For exemplary methodologiesin this regard, see Glick and Thompson, Methods in Plant MolecularBiology and Biotechnology, pp. 269-284 (CRC Press, Boca Raton, 1993).

Wang et al. discuss “Large Scale Identification, Mapping and Genotypingof Single-Nucleotide Polymorphisms in the Human Genome”, Science (1998)280:1077-1082, and similar capabilities are increasingly available forthe soybean genome. Map information concerning chromosomal location isuseful for proprietary protection of a subject transgenic plant. Ifunauthorized propagation is undertaken and crosses made with othergermplasm, the map of the integration region can be compared to similarmaps for suspect plants to determine if the latter have a commonparentage with the subject plant. Map comparisons could involvehybridizations, RFLP, PCR, SSR, sequencing or combinations thereof, allof which are conventional techniques. SNPs may also be used alone or incombination with other techniques.

Likewise, plants can be genetically engineered to express variousphenotypes of agronomic interest. Through the transformation of soybeanthe expression of genes can be altered to enhance disease resistance,insect resistance, herbicide resistance, agronomic, grain quality, andother traits. Transformation can also be used to insert DNA sequenceswhich control or help control male-sterility. DNA sequences native tosoybean as well as non-native DNA sequences can be transformed intosoybean and used to alter levels of native or non-native proteins.Various promoters, targeting sequences, enhancing sequences, and otherDNA sequences can be inserted into the genome for the purpose ofaltering the expression of proteins. Reduction of the activity ofspecific genes (also known as gene silencing or gene suppression) isdesirable for several aspects of genetic engineering in plants.

Many techniques for gene silencing are well known to one of skill in theart, including but not limited to, knock-outs (such as by insertion of atransposable element such as mu (Vicki Chandler, The Maize Handbook ch.118 (Springer-Verlag 1994); antisense technology (see, e.g., Sheehy etal. (1988) PNAS USA 85:8805-8809; and U.S. Pat. Nos. 5,107,065;5,453,566; and 5,759,829); co-suppression (e.g., Taylor (1997) PlantCell 9:1245; Jorgensen (1990) Trends Biotech. 8:340-344; Flavell (1994)PNAS USA 91:3490-3496; Finnegan et al. (1994) Bio/Technology 12:883-888;and Neuhuber et al. (1994) Mol. Gen. Genet. 244:230-241); RNAinterference (Napoli et al. (1990) Plant Cell 2:279-289; U.S. Pat. No.5,034,323; Sharp (1999) Genes Dev. 13:139-141; Zamore et al. (2000) Cell101:25-33; and Montgomery et al. (1998) PNAS USA 95:15502-15507);virus-induced gene silencing (Burton et al. (2000) Plant Cell12:691-705; and Baulcombe (1999) Curr. Op. Plant Biol. 2:109-113);target-RNA-specific ribozymes (Haseloff et al. (1988) Nature 334:585-591); hairpin structures (Smith et al. (2000) Nature 407:319-320; WO99/53050; and WO 98/53083); microRNA (Aukerman & Sakai (2003) Plant Cell15:2730-2741); ribozymes (Steinecke et al. (1992) EMBO J. 11:1525; andPerriman et al. (1993) Antisense Res. Dev. 3:253); oligonucleotidemediated targeted modification (e.g., WO 03/076574 and WO 99/25853);Zn-finger targeted molecules (e.g., WO 01/52620; WO 03/048345; and WO00/42219); and other methods or combinations of the above methods knownto those of skill in the art.

Exemplary nucleotide sequences that may be altered by geneticengineering include, but are not limited to, those categorized below.

1. Transgenes That Confer Resistance To Insects Or Disease And ThatEncode:

(A) Plant disease resistance genes. Plant defenses are often activatedby specific interaction between the product of a disease resistance gene(R) in the plant and the product of a corresponding avirulence (Avr)gene in the pathogen. A plant variety can be transformed with clonedresistance gene to engineer plants that are resistant to specificpathogen strains. See, for example Jones et al. (1994) Science 266: 789(cloning of the tomato Cf-9 gene for resistance to Cladosporium fulvum);Martin et al. (1993) Science 262:1432 (tomato Pto gene for resistance toPseudomonas syringae pv. tomato encodes a protein kinase); Mindrinos etal. (1994) Cell 78:1089 (Arabidopsis RPS2 gene for resistance toPseudomonas syringae), McDowell & Woffenden (2003) Trends Biotechnol.21:178-83; and Toyoda et al. (2002) Transgenic Res. 11:567-82. A plantresistant to a disease is one that is more resistant to a pathogen ascompared to the wild type plant.

(B) A Bacillus thuringiensis (Bt) protein, a derivative thereof or asynthetic polypeptide modeled thereon. See, for example, Geiser et al.(1986) Gene 48:109, who disclose the cloning and nucleotide sequence ofa Bt delta-endotoxin gene. Moreover, DNA molecules encodingdelta-endotoxin genes can be purchased from American Type CultureCollection (Rockville, Md.), for example, under ATCC Accession Nos.40098, 67136, 31995, and 31998. Other non-limiting examples of Bacillusthuringiensis transgenes being genetically engineered are given in thefollowing patents and patent applications, and hereby are incorporatedby reference for this purpose: U.S. Pat. Nos. 5,188,960; 5,689,052;5,880,275; 5,986,177; 7,105,332; 7,208,474; WO 91/14778; WO 99/31248; WO01/12731; WO 99/24581; WO 97/40162; US2002/0151709; US2003/0177528;US2005/0138685; US/20070245427; US2007/0245428; US2006/0241042;US2008/0020966; US2008/0020968; US2008/0020967; US2008/0172762;US2008/0172762; and US2009/0005306.

(C) An insect-specific hormone or pheromone such as an ecdysteroid orjuvenile hormone, a variant thereof, a mimetic based thereon, or anantagonist or agonist thereof. See, for example, the disclosure byHammock et al. (1990) Nature 344:458, of baculovirus expression ofcloned juvenile hormone esterase, an inactivator of juvenile hormone.

(D) An insect-specific peptide which, upon expression, disrupts thephysiology of the affected pest. For example, see the disclosures ofRegan (1994) J. Biol. Chem. 269:9 (expression cloning yields DNA codingfor insect diuretic hormone receptor); Pratt et al. (1989) Biochem.Biophys. Res. Comm. 163:1243 (an allostatin is identified in Diplopterapuntata); Chattopadhyay et al. (2004) Critical Reviews in Microbiology30:33-54 2004; Zjawiony (2004) J Nat Prod 67:300-310; Carlini &Grossi-de-Sa (2002) Toxicon 40:1515-1539; Ussuf et al. (2001) Curr Sci.80:847-853; and Vasconcelos & Oliveira (2004) Toxicon 44:385-403. Seealso U.S. Pat. No. 5,266,317 to Tomalski et al., who disclose genesencoding insect-specific toxins.

(E) An enzyme responsible for a hyperaccumulation of a monoterpene, asesquiterpene, a steroid, hydroxamic acid, a phenylpropanoid derivative,or another non-protein molecule with insecticidal activity.

(F) An enzyme involved in the modification, including thepost-translational modification, of a biologically active molecule; forexample, a glycolytic enzyme, a proteolytic enzyme, a lipolytic enzyme,a nuclease, a cyclase, a transaminase, an esterase, a hydrolase, aphosphatase, a kinase, a phosphorylase, a polymerase, an elastase, achitinase and a glucanase, whether natural or synthetic. See WO93/02197, which discloses the nucleotide sequence of a callase gene. DNAmolecules which contain chitinase-encoding sequences can be obtained,for example, from the ATCC under Accession Nos. 39637 and 67152. Seealso Kramer et al. (1993) Insect Biochem. Molec. Biol. 23:691, who teachthe nucleotide sequence of a cDNA encoding tobacco hookworm chitinase,and Kawalleck et al. (1993) Plant Mol. Biol. 21:673, who provide thenucleotide sequence of the parsley ubi4-2 polyubiquitin gene, and U.S.Pat. Nos. 6,563,020; 7,145,060; and 7,087,810.

(G) A molecule that stimulates signal transduction. For example, see thedisclosure by Botella et al. (1994) Plant Mol. Biol. 24:757, ofnucleotide sequences for mung bean calmodulin cDNA clones, and Griess etal. (1994) Plant Physio1.104:1467, which provides the nucleotidesequence of a maize calmodulin cDNA clone.

(H) A hydrophobic moment peptide. See WO 95/16776 and U.S. Pat. No.5,580,852 disclosure of peptide derivatives of tachyplesin which inhibitfungal plant pathogens, and WO 95/18855 and U.S. Pat. No. 5,607,914which teach synthetic antimicrobial peptides that confer diseaseresistance.

(I) A membrane permease, a channel former, or a channel blocker. Forexample, see the disclosure by Jaynes et al. (1993) Plant Sci. 89:43, ofheterologous expression of a cecropin-beta lytic peptide analog torender transgenic tobacco plants resistant to Pseudomonas solanacearum.

(J) A viral-invasive protein or a complex toxin derived therefrom. Forexample, the accumulation of viral coat proteins in transformed plantcells imparts resistance to viral infection and/or disease developmenteffected by the virus from which the coat protein gene is derived, aswell as by related viruses. See Beachy et al. (1990) Ann. Rev.Phytopathol. 28:451. Coat protein-mediated resistance has been conferredupon transformed plants against alfalfa mosaic virus, cucumber mosaicvirus, tobacco streak virus, potato virus X, potato virus Y, tobaccoetch virus, tobacco rattle virus, and tobacco mosaic virus.

(K) An insect-specific antibody or an immunotoxin derived therefrom.Thus, an antibody targeted to a critical metabolic function in theinsect gut would inactivate an affected enzyme, killing the insect. Cf.Taylor et al., Abstract #497, Seventh Int'l Symposium on MolecularPlant-Microbe Interactions (Edinburgh, Scotland, 1994) (enzymaticinactivation in transgenic tobacco via production of single-chainantibody fragments).

(L) A virus-specific antibody. See, for example, Tavladoraki et al.(1993) Nature 366:469, who show that transgenic plants expressingrecombinant antibody genes are protected from virus attack.

(M) A developmental-arrestive protein produced in nature by a pathogenor a parasite. Thus, fungal endo alpha-1,4-D-polygalacturonasesfacilitate fungal colonization and plant nutrient release bysolubilizing plant cell wall homo-alpha-1,4-D-galacturonase. See Lamb etal. (1992) Bio/Technology 10:1436. The cloning and characterization of agene which encodes a bean endopolygalacturonase-inhibiting protein isdescribed by Toubart et al. (1992) Plant J. 2:367.

(N) A developmental-arrestive protein produced in nature by a plant. Forexample, Logemann et al. (1992) Bio/Technology 10:305, have shown thattransgenic plants expressing the barley ribosome-inactivating gene havean increased resistance to fungal disease.

(O) Genes involved in the systemic acquired resistance (SAR) Responseand/or the pathogenesis related genes. Briggs (1995) Current Biology5:128-131, Pieterse & Van Loon (2004) Curr. Opin. Plant Bio. 7:456-64;and Somssich (2003) Cell 113:815-6.

-   -   (P) Antifungal genes (Cornelissen and Melchers (1993) Plant        Physiol. 101:709-712; Parijs et al. (1991) Planta 183:258-264;        Bushnell et al. (1998) Can. J. Plant Path. 20:137-149. Also, see        US2002/0166141; US2007/0274972; US2007/0192899; US2008/0022426;        and U.S. Pat. Nos. 6,891,085; 7,306,946; and 7,598,346.    -   (Q) Detoxification genes, such as for fumonisin, beauvericin,        moniliformin, zearalenone, and their structurally related        derivatives. For example, see U.S. Pat. Nos. 5,716,820;        5,792,931; 5,798,255; 5,846,812; 6,083,736; 6,538,177;        6,388,171; and 6,812,380.

(R) Cystatin and cysteine proteinase inhibitors. See U.S. Pat. No.7,205,453.

(S) Defensin genes. See WO 03/000863 and U.S. Pat. Nos. 6,911,577;6,855,865; 6,777,592; and 7,238,781.

(T) Genes conferring resistance to nematodes. See e.g. WO 96/30517; WO93/19181; WO 03/033651; and Urwin et al. (1998) Planta 204:472-479;Williamson (1999) Curr Opin Plant Bio. 2:327-31; and U.S. Pat. Nos.6,284,948 and 7,301,069.

(U) Genes that confer resistance to Phytophthora Root Rot, such as Rps1,Rps1-a, Rps1-b, Rps1-c, Rps1-d, Rps1-e, Rps1-k, Rps2, Rps3-a, Rps3-b,Rps3-c, Rps4, Rps5, Rps6, Rps7, Rps8, and other Rps genes. See, forexample, Shoemaker et al. “Phytophthora Root Rot Resistance Gene Mappingin Soybean”, Plant Genome IV Conference, San Diego, Calif. (1995).

(V) Genes that confer resistance to Brown Stem Rot, such as described inU.S. Pat. No. 5,689,035, and incorporated by reference for this purpose.

2. Transgenes That Confer Resistance To A Herbicide, For Example:

(A) A herbicide that inhibits the growing point or meristem, such as animidazolinone, or a sulfonylurea. Exemplary genes include mutant ALS andAHAS enzymes as described, for example, by Lee et al. (1988) EMBO J.7:1241; and, Miki et al. (1990) Theor. Appl. Genet. 80:449,respectively. See also, U.S. Pat. Nos. 5,605,011; 5,013,659; 5,141,870;5,767,361; 5,731,180; 5,304,732; 4,761,373; 5,331,107; 5,928,937; and5,378,824; US2007/0214515; and WO 96/33270.

(B) Glyphosate (resistance imparted by mutant5-enolpyruvl-3-phosphikimate synthase (EPSP) and aroA genes,respectively) and other phosphono compounds such as glufosinate(phosphinothricin acetyl transferase (PAT) and Streptomyceshygroscopicus phosphinothricin acetyl transferase (bar) genes), andpyridinoxy or phenoxy proprionic acids and cyclohexones (ACCaseinhibitor-encoding genes). See, for example, U.S. Pat. No. 4,940,835 toShah et al., which discloses the nucleotide sequence of a form of EPSPSwhich can confer glyphosate resistance. U.S. Pat. No. 5,627,061 to Barryet al. also describes genes encoding EPSPS enzymes. See also U.S. Pat.Nos. 6,566,587; 6,338,961; 6,248,876; 6,040,497; 5,804,425; 5,633,435;5,145,783; 4,971,908; 5,312,910; 5,188,642; 4,940,835; 5,866,775;6,225,114; 6,130,366; 5,310,667; 4,535,060; 4,769,061; 5,633,448;5,510,471; RE 36,449; RE 37,287; and 5,491,288; and. EP1173580; WO01/66704; EP1173581; and EP1173582, which are incorporated herein byreference for this purpose. Glyphosate resistance is also imparted toplants that express a gene that encodes a glyphosate oxido-reductaseenzyme as described more fully in U.S. Pat. Nos. 5,776,760 and5,463,175, which are incorporated herein by reference for this purpose.In addition, glyphosate resistance can be imparted to plants by theoverexpression of genes encoding glyphosate N-acetyltransferase. See,for example, US2004/0082770; US2005/0246798; and US2008/0234130 whichare incorporated herein by reference for this purpose. A DNA moleculeencoding a mutant aroA gene can be obtained under ATCC accession No.39256, and the nucleotide sequence of the mutant gene is disclosed inU.S. Pat. No. 4,769,061 to Comai. European Patent Application No. 0 333033 to Kumada et al. and U.S. Pat. No. 4,975,374 to Goodman et al.disclose nucleotide sequences of glutamine synthetase genes which conferresistance to herbicides such as L-phosphinothricin. The nucleotidesequence of a phosphinothricin-acetyl-transferase gene is provided inEuropean Patent No. 0 242 246 and 0 242 236 to Leemans et al. De Greefet al. (1989) Bio/Technology 7:61 describe the production of transgenicplants that express chimeric bar genes coding for phosphinothricinacetyl transferase activity. See also, U.S. Pat. Nos. 5,969,213;5,489,520; 5,550,318; 5,874,265; 5,919,675; 5,561,236; 5,648,477;5,646,024; 6,177,616; and 5,879,903, which are incorporated herein byreference for this purpose. Exemplary genes conferring resistance tophenoxy proprionic acids and cyclohexones, such as sethoxydim andhaloxyfop, are the Acc1-S1, Acc1-S2, and Acc1-S3 genes described byMarshall et al. (1992) Theor. Appl. Genet. 83:435.

(C) A herbicide that inhibits photosynthesis, such as a triazine (psbAand gs+ genes) and a benzonitrile (nitrilase gene). Przibilla et al.(1991) Plant Cell 3:169, describe the transformation of Chlamydomonaswith plasmids encoding mutant psbA genes. Nucleotide sequences fornitrilase genes are disclosed in U.S. Pat. No. 4,810,648, and DNAmolecules containing these genes are available under ATCC Accession Nos.53435, 67441, and 67442. Cloning and expression of DNA coding for aglutathione S-transferase is described by Hayes et al. (1992) Biochem.J. 285:173.

(D) Acetohydroxy acid synthase, which has been found to make plants thatexpress this enzyme resistant to multiple types of herbicides, has beenintroduced into a variety of plants (see, e.g., Hattori et al. (1995)Mol Gen Genet 246:419). Other genes that confer resistance to herbicidesinclude: a gene encoding a chimeric protein of rat cytochrome P4507A1and yeast NADPH-cytochrome P450 oxidoreductase (Shiota et al. (1994)Plant Physiol 106:17), genes for glutathione reductase and superoxidedismutase (Aono et al. (1995) Plant Cell Physiol 36:1687), and genes forvarious phosphotransferases (Datta et al. (1992) Plant Mol Biol 20:619).

(E) Protoporphyrinogen oxidase (protox) is necessary for the productionof chlorophyll, which is necessary for all plant survival. The protoxenzyme serves as the target for a variety of herbicidal compounds. Theseherbicides also inhibit growth of all the different species of plantspresent, causing their total destruction. The development of plantscontaining altered protox activity which are resistant to theseherbicides are described in U.S. Pat. No. 6,288,306; 6,282,837; and5,767,373; and WO 01/12825.

3. Transgenes That Confer Or Contribute To a Grain And/Or SeedCharacteristic, Such As:

(A) Fatty acid profile(s), for example, by

-   -   (1) Down-regulation of stearoyl-ACP desaturase to increase        stearic acid content of the plant. See Knultzon et al. (1992)        Proc. Natl. Acad. Sci. USA 89:2624; and WO 99/64579 (Genes for        Desaturases to Alter Lipid Profiles in Corn).    -   (2) Elevating oleic acid via FAD-2 gene modification and/or        decreasing linolenic acid via FAD-3 gene modification (see U.S.        Pat. Nos. 6,063,947; 6,323,392; 6,372,965; and WO 93/11245).    -   (3) Altering conjugated linolenic or linoleic acid content, such        as in WO 01/12800.    -   (4) Altering LEC1, AGP, mi1ps, and various 1pa genes such as        Ipa1, Ipa3, hpt or hggt. For example, see WO 02/42424; WO        98/22604; WO 03/011015; U.S. Pat. Nos. 6,423,886; 6,197,561;        and, 6,825,397; US2003/0079247; US2003/0204870; WO 02/057439; WO        03/011015; and Rivera-Madrid et al. (1995) Proc. Natl. Acad.        Sci. 92:5620-5624.

B) Altered phosphorus content, for example, by:

-   -   (1) Introduction of a phytase-encoding gene would enhance        breakdown of phytate, adding more free phosphate to the        transformed plant. For example, see Van Hartingsveldt et        al. (1993) Gene 127:87, for a disclosure of the nucleotide        sequence of an Aspergillus niger phytase gene.    -   (2) Modulating a gene that reduces phytate content. For example        in maize this could be accomplished by cloning and then        re-introducing DNA associated with one or more of the alleles,        such as the LPA alleles, identified in maize mutants        characterized by low levels of phytic acid, such as in WO        05/113778; and/or by altering inositol kinase activity as in WO        02/059324; U.S. Pat. No. 7,067,720; WO 03/027243;        US2003/0079247; WO 99/05298; U.S. Pat. Nos. 6,197,561;        6,291,224; and 6,391,348; WO 98/45448; WO 99/55882; and WO        01/04147.

(C) Altered carbohydrates, for example, by altering a gene for an enzymethat affects the branching pattern of starch or, a gene alteringthioredoxin such as NTR and/or TRX (see U.S. Pat. No. 6,531,648 which isincorporated by reference for this purpose). See Shiroza et al. (1988)J. Bacteriol. 170:810 (nucleotide sequence of Streptococcus mutansfructosyltransferase gene); Steinmetz et al. (1985) Mol. Gen. Genet.200:220 (nucleotide sequence of Bacillus subtilis levansucrase gene);Pen et al. (1992) Bio/Technology 10:292 (production of transgenic plantsthat express Bacillus licheniformis alpha-amylase); Elliot et al. (1993)Plant Mol. Biol. 21:515 (nucleotide sequences of tomato invertasegenes); Søgaard et al. (1993) J. Biol. Chem. 268:22480 (site-directedmutagenesis of barley alpha-amylase gene); Fisher et al. (1993) PlantPhysiol. 102:1045 (maize endosperm starch branching enzyme II); WO99/10498 (improved digestibility and/or starch extraction throughmodification of UDP-D-xylose 4-epimerase, Fragile 1 and 2, Reft HCHL,C4H); and, U.S. Pat. No. 6,232,529 (method of producing high oil seed bymodification of starch levels (AGP). The fatty acid modification genesmentioned herein may also be used to affect starch content and/orcomposition through the interrelationship of the starch and oilpathways.

(D) Altered antioxidant content or composition, such as alteration oftocopherol or tocotrienols. For example, see U.S. Pat. Nos. 6,787,683;7,154,029; and WO 00/68393 involving the manipulation of antioxidantlevels, and WO 03/082899 through alteration of a homogentisate geranylgeranyl transferase (hggt).

(E) Altered essential seed amino acids. For example, see U.S. Pat. No.6,127,600 (method of increasing accumulation of essential amino acids inseeds); U.S. Pat. No. 6,080,913 (binary methods of increasingaccumulation of essential amino acids in seeds); U.S. Pat. No. 5,990,389(high lysine); WO 99/40209 (alteration of amino acid compositions inseeds); WO 99/29882 (methods for altering amino acid content ofproteins); U.S. Pat. No. 5,850,016 (alteration of amino acidcompositions in seeds); WO 98/20133 (proteins with enhanced levels ofessential amino acids); U.S. Pat. No. 5,885,802 (high methionine); U.S.Pat. No. 5,885,801 (high threonine); U.S. Pat. No. 6,664,445 (plantamino acid biosynthetic enzymes); U.S. Pat. No. 6,459,019 (increasedlysine and threonine); U.S. Pat. No. 6,441,274 (plant tryptophansynthase beta subunit); U.S. Pat. No. 6,346,403 (methionine metabolicenzymes); U.S. Pat. No. 5,939,599 (high sulfur); U.S. Pat. No. 5,912,414(increased methionine); WO 98/56935 (plant amino acid biosyntheticenzymes); WO 98/45458 (engineered seed protein having higher percentageof essential amino acids); WO 98/42831 (increased lysine); U.S. Pat. No.5,633,436 (increasing sulfur amino acid content); U.S. Pat. No.5,559,223 (synthetic storage proteins with defined structure containingprogrammable levels of essential amino acids); WO 96/01905 (increasedthreonine); WO 95/15392 (increased lysine); U.S. Pat. Nos. 6,930,225;7,179,955; 6,803,498; US2004/0068767; and WO 01/79516.

4. Genes that Control Male-sterility

There are several methods of conferring genetic male sterilityavailable, such as multiple mutant genes at separate locations withinthe genome that confer male sterility, as disclosed in U.S. Pat. Nos.4,654,465 and 4,727,219 to Brar et al., and chromosomal translocationsas described by Patterson in U.S. Pat. Nos. 3,861,709 and 3,710,511. Inaddition to these methods, Albertsen et al. U.S. Pat. No. 5,432,068,describe a system of nuclear male sterility which includes: identifyinga gene which is critical to male fertility; silencing this native genewhich is critical to male fertility; removing the native promoter fromthe essential male fertility gene and replacing it with an induciblepromoter; inserting this genetically engineered gene back into theplant; and thus creating a plant that is male sterile because theinducible promoter is not “on” resulting in the male fertility gene notbeing transcribed. Fertility is restored by inducing, or turning “on”,the promoter, which in turn allows the gene that confers male fertilityto be transcribed. Male sterile soybean lines and characterization arediscussed in Palmer (2000) Crop Sci 40:78-83, and Jin et al. (1997) SexPlant Reprod 10:13-21.

(A) Introduction of a deacetylase gene under the control of atapetum-specific promoter and with the application of the chemicalN-Ac-PPT (WO 01/29237).

(B) Introduction of various stamen-specific promoters (WO 92/13956 andWO 92/13957).

(C) Introduction of the barnase and the barstar gene (Paul et al. (1992)Plant Mol. Biol. 19:611-622).

For additional examples of nuclear male and female sterility systems andgenes, see also, U.S. Pat. Nos. 5,859,341; 6,297,426; 5,478,369;5,824,524; 5,850,014; and 6,265,640; all of which are herebyincorporated by reference.

5. Polynucleotides comprising a sequence for site specific DNArecombination. This includes the introduction of at least one FRT sitethat may be used in the FLP/FRT system and/or a Lox site that may beused in the Cre/Lox system. For example, see Lyznik et al. (2003) PlantCell Rep 21:925-932; and WO 99/25821, which are hereby incorporated byreference. Other systems that may be used include the Gin recombinase ofphage Mu (Maeser et al. (1991) Mol Gen Genet 230:170-176); the Pinrecombinase of E. coli (Enomoto et al. (1983) J Bacteriol 156:663-668);and the R/RS system of the pSR1 plasmid (Araki et al. (1992) J Mol Biol182:191-203).6. Genes that affect abiotic stress resistance (including but notlimited to flowering, flower development, pod, and seed development,enhancement of nitrogen utilization efficiency, altered nitrogenresponsiveness, drought resistance or tolerance, cold resistance ortolerance, and salt resistance or tolerance) and increased yield understress. For example, see WO 00/73475 where water use efficiency isaltered through alteration of malate; U.S. Pat. Nos. 5,892,009;5,965,705; 5,929,305; 5,891,859; 6,417,428; 6,664,446; 6,706,866;6,717,034; and 6,801,104; WO 00/060089; WO 01/026459; WO 00/1035725; WO01/034726; WO 01/035727; WO 00/1036444; WO 01/036597; WO 01/036598; WO00/2015675; WO 02/017430; WO 02/077185; WO 02/079403; WO 03/013227; WO03/013228; WO 03/014327; WO 04/031349; WO 04/076638; WO 98/09521; and WO99/38977 describing genes, including CBF genes (C-repeat/DRE-BindingFactor, see, e.g., Stockinger et al. 1997 PNAS 94:1035-1040) andtranscription factors effective in mitigating the negative effects offreezing, high salinity, and drought on plants, as well as conferringother positive effects on plant phenotype; US2004/0148654 and WO01/36596 where abscisic acid is altered in plants resulting in improvedplant phenotype such as increased yield and/or increased tolerance toabiotic stress; WO 00/006341, WO 04/090143, U.S. Patents 7,531,723, and6,992,237 where cytokinin expression is modified resulting in plantswith increased stress tolerance, such as drought tolerance, and/orincreased yield. Also see WO 02/02776, WO 03/052063, JP2002281975, U.S.Pat. No. 6,084,153, WO 01/64898, U.S. Pat. No. 6,177,275, and U.S. Pat.No. 6,107,547 (enhancement of nitrogen utilization and altered nitrogenresponsiveness). For ethylene alteration, see US2004/0128719,US2003/0166197, and WO 00/32761. For plant transcription factors ortranscriptional regulators of abiotic stress, see e.g. US2004/0098764 orUS2004/0078852.

Other genes and transcription factors that affect plant growth andagronomic traits such as yield, flowering, plant growth, and/or plantstructure, can be introduced or introgressed into plants, see e.g., WO97/49811 (LHY), WO 98/56918 (ESD4), WO 97/10339, and U.S. Pat. No.6,573,430 (TFL), U.S. Pat. No. 6,713,663 (FT), WO 96/14414 (CON), WO96/38560, WO 01/21822 (VRN1), WO 00/44918 (VRN2), WO 99/49064 (GI), WO00/46358 (FRI), WO 97/29123, U.S. Pat. No. 6,794,560, U.S. Pat. No.6,307,126 (GAI), WO 99/09174 (D8 and Rht), and WO 04/076638 and WO04/031349 (transcription factors).

Development of Soybean Sublines

Sublines of XB39AE12 may also be developed and are provided. AlthoughXB39AE12 contains substantially fixed genetics and is phenotypicallyuniform with no off-types expected, there still remains a smallproportion of segregating loci either within individuals or within thepopulation as a whole. Sublining provides the ability to select forthese loci, which have no apparent morphological or phenotypic effect onthe plant characteristics, but may have an effect on overall yield. Forexample, the methods described in U.S. Pat. Nos. 5,437,697, 7,973,212,and US2011/0258733, and US2011/0283425 (each of which is hereinincorporated by reference) may be utilized by a breeder of ordinaryskill in the art to identify genetic loci that are associated with yieldpotential to further purify the variety in order to increase its yield.A breeder of ordinary skill in the art may fix agronomically importantloci by making them homozygous in order to optimize the performance ofthe variety. The development of soybean sublines and the use ofaccelerated yield technology is a plant breeding technique.

Soybean varieties such as XB39AE12 are typically developed for use inseed and grain production. However, soybean varieties such as XB39AE12also provide a source of breeding material that may be used to developnew soybean varieties. Plant breeding techniques known in the art andused in a soybean plant breeding program include, but are not limitedto, recurrent selection, mass selection, bulk selection, backcrossing,pedigree breeding, open pollination breeding, restriction fragmentlength polymorphism enhanced selection, genetic marker enhancedselection, making double haploids, and transformation. Oftencombinations of these techniques are used. The development of soybeanvarieties in a plant breeding program requires, in general, thedevelopment and evaluation of homozygous varieties. There are manyanalytical methods available to evaluate a new variety. The oldest andmost traditional method of analysis is the observation of phenotypictraits but genotypic analysis may also be used.

Methods for producing a soybean plant by crossing a first parent soybeanplant with a second parent soybean plant wherein the first and/or secondparent soybean plant is variety XB39AE12 are provided. Also provided aremethods for producing a soybean plant having substantially all of themorphological and physiological characteristics of variety XB39AE12, bycrossing a first parent soybean plant with a second parent soybean plantwherein the first and/or the second parent soybean plant is a planthaving substantially all of the morphological and physiologicalcharacteristics of variety XB39AE12 set forth in Table 1, as determinedat the 5% significance level when grown in the same environmentalconditions. The other parent may be any soybean plant, such as a soybeanplant that is part of a synthetic or natural population. Any suchmethods using soybean variety XB39AE12 include but are not limited toselfing, sibbing, backcrossing, mass selection, pedigree breeding, bulkselection, hybrid production, crossing to populations, and the like.These methods are well known in the art and some of the more commonlyused breeding methods are described below. Descriptions of breedingmethods can be found in one of several reference books (e.g., Allard,Principles of Plant Breeding, 1960; Simmonds, Principles of CropImprovement, 1979; Fehr, “Breeding Methods for Cultivar Development”,Chapter 7, Soybean Improvement, Production and Uses, 2^(nd) ed., Wilcoxeditor, 1987).

Pedigree breeding starts with the crossing of two genotypes, such asXB39AE12 or a soybean variety having all of the morphological andphysiological characteristics of XB39AE12, and another soybean varietyhaving one or more desirable characteristics that is lacking or whichcomplements XB39AE12. If the two original parents do not provide all thedesired characteristics, other sources can be included in the breedingpopulation. In the pedigree method, superior plants are selfed andselected in successive filial generations. In the succeeding filialgenerations, the heterozygous allele condition gives way to thehomozygous allele condition as a result of inbreeding. Typically in thepedigree method of breeding, five or more successive filial generationsof selfing and selection are practiced: e.g., F1→F2; F2→F3; F3→F4;F4→F5; etc. In some examples, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or moregenerations of selfing and selection are practiced. After a sufficientamount of inbreeding, successive filial generations will serve toincrease seed of the developed variety. Typically, the developed varietycomprises homozygous alleles at about 95% or more of its loci.

In addition to being used to create backcross conversion populations,backcrossing can also be used in combination with pedigree breeding. Asdiscussed previously, backcrossing can be used to transfer one or morespecifically desirable traits from one variety (the donor parent) to adeveloped variety (the recurrent parent), which has good overallagronomic characteristics yet may lack one or more other desirabletraits. However, the same procedure can be used to move the progenytoward the genotype of the recurrent parent but at the same time retainmany components of the non-recurrent parent by stopping the backcrossingat an early stage and proceeding with selfing and selection. Forexample, a soybean variety may be crossed with another variety toproduce a first generation progeny plant. The first generation progenyplant may then be backcrossed to one of its parent varieties to create aBC1F1. Progeny are selfed and selected so that the newly developedvariety has many of the attributes of the recurrent parent and yetseveral of the desired attributes of the donor parent. This approachleverages the value and strengths of both parents for use in new soybeanvarieties.

Therefore, in some examples a method of making a backcross conversion ofsoybean variety XB39AE12, comprising the steps of crossing a plant ofsoybean variety XB39AE12 or a soybean variety having all of themorphological and physiological characteristics of XB39AE12 with a donorplant possessing a desired trait to introduce the desired trait,selecting an F1 progeny plant containing the desired trait, andbackcrossing the selected F1 progeny plant to a plant of soybean varietyXB39AE12 are provided. This method may further comprise the step ofobtaining a molecular marker profile of soybean variety XB39AE12 andusing the molecular marker profile to select for a progeny plant withthe desired trait and the molecular marker profile of XB39AE12. Themolecular marker profile can comprise information from one or moremarkers. In one example the desired trait is a mutant gene or transgenepresent in the donor parent. In another example, the desired trait is anative trait in the donor parent.

Recurrent selection is a method used in a plant breeding program toimprove a population of plants. Variety XB39AE12, and/or a soybeanvariety having all of the morphological and physiologicalcharacteristics of XB39AE12, is suitable for use in a recurrentselection program. The method entails individual plants crosspollinating with each other to form progeny. The progeny are grown andthe superior progeny selected by any number of selection methods, whichinclude individual plant, half-sib progeny, full-sib progeny, and selfedprogeny. The selected progeny are cross pollinated with each other toform progeny for another population. This population is planted and,again, superior plants are selected to cross pollinate with each other.Recurrent selection is a cyclical process and therefore can be repeatedas many times as desired. The objective of recurrent selection is toimprove the traits of a population. The improved population can then beused as a source of breeding material to obtain new varieties forcommercial or breeding use, including the production of a syntheticcultivar. A synthetic cultivar is the resultant progeny formed by theintercrossing of several selected varieties.

Mass selection is a useful technique when used in conjunction withmolecular marker enhanced selection. In mass selection, seeds fromindividuals are selected based on phenotype or genotype. These selectedseeds are then bulked and used to grow the next generation. Bulkselection requires growing a population of plants in a bulk plot,allowing the plants to self-pollinate, harvesting the seed in bulk, andthen using a sample of the seed harvested in bulk to plant the nextgeneration. Also, instead of self pollination, directed pollinationcould be used as part of the breeding program.

Mutation breeding is another method of introducing new traits intosoybean variety XB39AE12 or a soybean variety having all of themorphological and physiological characteristics of XB39AE12. Mutationsthat occur spontaneously or that are artificially induced can be usefulsources of variability for a plant breeder. The goal of artificialmutagenesis is to increase the rate of mutation for a desiredcharacteristic. Mutation rates can be increased by many different meansincluding temperature, long-term seed storage, tissue cultureconditions, radiation; such as X-rays, gamma rays (e.g., cobalt 60 orcesium 137), neutrons, (product of nuclear fission by uranium 235 in anatomic reactor), beta radiation (emitted from radioisotopes such asphosphorus 32 or carbon 14), ultraviolet radiation (preferably from 2500to 2900 nm), or chemical mutagens such as base analogues(5-bromo-uracil), related compounds (8-ethoxy caffeine), antibiotics(streptonigrin), alkylating agents (sulfur mustards, nitrogen mustards,epoxides, ethylenamines, sulfates, sulfonates, sulfones, lactones),azide, hydroxylamine, nitrous acid, or acridines. Once a desired traitis observed through mutagenesis, the trait may then be incorporated intoexisting germplasm by traditional breeding techniques. Details ofmutation breeding can be found in “Principles of Cultivar Development”Fehr, 1993, Macmillan Publishing Company. In addition, mutations createdin other soybean plants may be used to produce a backcross conversion ofXB39AE12 that comprises such mutation.

Molecular markers, which include markers identified through the use oftechniques such as isozyme electrophoresis, restriction fragment lengthpolymorphisms (RFLPs), randomly amplified polymorphic DNAs (RAPDs),arbitrarily primed polymerase chain reaction (AP-PCR), DNA amplificationfingerprinting (DAF), sequence characterized amplified regions (SCARs),amplified fragment length polymorphisms (AFLPs), simple sequence repeats(SSRs), and single nucleotide polymorphisms (SNPs), may be used in plantbreeding methods utilizing XB39AE12.

Isozyme electrophoresis and RFLPs have been widely used to determinegenetic composition. Shoemaker and Olsen (“Molecular Linkage Map ofSoybean (Glycine max L. Merr.)”, p. 6.131-6.138. In S. J. O'Brien (ed.)Genetic Maps: Locus Maps of Complex Genomes. (1993) Cold Spring HarborLaboratory Press. Cold Spring Harbor, N.Y.), developed a moleculargenetic linkage map that consisted of 25 linkage groups with about 365RFLP, 11 RAPD (random amplified polymorphic DNA), three classicalmarkers, and four isozyme loci. See also, Shoemaker “RFLP Map ofSoybean”. pp 299-309 (1994). In R. L. Phillips and I. K. Vasil (ed.)DNA-based markers in plants. Kluwer Academic Press Dordrecht, theNetherlands.

SSR technology is an efficient and practical marker technology; moremarker loci can be routinely used and more alleles per marker locus canbe found using SSRs in comparison to RFLPs. For example, Diwan andCregan, described highly polymorphic microsatellite loci in soybean withas many as 26 alleles. (Diwan and Cregan (1997) Theor. Appl. Genet.95:220-225). Single nucleotide polymorphisms (SNPs) may also be used toidentify the unique genetic composition of the XB39AE12 and progenyvarieties retaining or derived from that unique genetic composition.Various molecular marker techniques may be used in combination toenhance overall resolution.

Soybean DNA molecular marker linkage maps have been rapidly constructedand widely implemented in genetic studies. One such study is describedin Cregan et al. (1999) Crop Science 39:1464-1490. Sequences and PCRconditions of SSR loci in soybean, as well as the most current geneticmap, may be found in Soybase on the world wide web.

One use of molecular markers is quantitative trait loci (QTL) mapping.QTL mapping is the use of markers which are known to be closely linkedto alleles that have measurable effects on a quantitative trait.Selection in the breeding process is based upon the accumulation ofmarkers linked to the positive effecting alleles and/or the eliminationof the markers linked to the negative effecting alleles from the plantgenome.

Molecular markers can also be used during the breeding process for theselection of qualitative traits. For example, markers closely linked toalleles or markers containing sequences within the actual alleles ofinterest can be used to select plants that contain the alleles ofinterest during a backcrossing breeding program. The markers can also beused to select for the genome of the recurrent parent and against thegenome of the donor parent. Using this procedure can minimize the amountof genome from the donor parent that remains in the selected plants. Itcan also be used to reduce the number of crosses back to the recurrentparent needed in a backcrossing program. The use of molecular markers inthe selection process is often called genetic marker enhanced selection.

Production of Double Haploids

The production of double haploids can also be used for the developmentof plants with a homozygous phenotype in the breeding program. Forexample, a soybean plant for which variety XB39AE12 or a soybean varietyhaving all of the morphological and physiological characteristics ofXB39AE12 is a parent can be used to produce double haploid plants.Double haploids are produced by the doubling of a set of chromosomes (1N) from a heterozygous plant to produce a completely homozygousindividual. For example, see Wan et al., “Efficient Production ofDoubled Haploid Plants Through Colchicine Treatment of Anther-DerivedMaize Callus” (1989) Theor Appl Genet 77:889-892, and US2003/0005479.This can be advantageous because the process omits the generations ofselfing needed to obtain a homozygous plant from a heterozygous source.

Methods for obtaining haploid plants are disclosed in Kobayashi et al.(1980) J Heredity 71:9-14; Pollacsek (1992) Agronomie (Paris)12:247-251; Cho-Un-Haing et al. (1996) J Plant Biol. 39:185-188;Verdoodt et al. (1998) Theor Appl Genet 96:294-300; Genetic Manipulationin Plant Breeding, Proceedings International Symposium Organized byEUCARPIA, Sep. 8-13, 1985, Berlin, Germany; Chalyk et al. (1994) MaizeGenet Coop. Newsletter 68:47. Double haploid technology in soybean isdiscussed in Croser et al. (2006) Crit Rev Plant Sci 25:139-157; andRodrigues et al. (2006) Brazilian Arc Biol Tech 49:537-545.

In some examples a process for making a substantially homozygousXB39AE12 progeny plant by producing or obtaining a seed from the crossof XB39AE12 and another soybean plant and applying double haploidmethods to the F1 seed or F1 plant or to any successive filialgeneration is provided. Based on studies in maize, and currently beingconducted in soybean, such methods would decrease the number ofgenerations required to produce a variety with similar genetics orcharacteristics to XB39AE12. See Bernardo and Kahler (2001) Theor. Appl.Genet. 102:986-992.

In particular, a process of making seed retaining the molecular markerprofile of soybean variety XB39AE12 is contemplated, such processcomprising obtaining or producing F1 seed for which soybean varietyXB39AE12 is a parent, inducing doubled haploids to create progenywithout the occurrence of meiotic segregation, obtaining the molecularmarker profile of soybean variety XB39AE12, and selecting progeny thatretain the molecular marker profile of XB39AE12.

Methods using seeds, plants, cells, or plant parts of variety XB39AE12in tissue culture are provided, as are the cultures, plants, parts,cells, and/or seeds derived therefrom. Tissue culture of various tissuesof soybeans and regeneration of plants therefrom is well known andwidely published. For example, see Komatsuda et al. (1991) Crop Sci.31:333-337; Stephens et al. “Agronomic Evaluation ofTissue-Culture-Derived Soybean Plants” (1991) Theor. Appl. Genet.82:633-635; Komatsuda et al. “Maturation and Germination of SomaticEmbryos as Affected by Sucrose and Plant Growth Regulators in SoybeansGlycine gracilis Skvortz and Glycine max (L.) Merr.” (1992) Plant CellTissue and Organ Culture 28:103-113; Dhir et al. “Regeneration ofFertile Plants from Protoplasts of Soybean (Glycine max L. Merr.):Genotypic Differences in Culture Response” (1992) Plant Cell Reports11:285-289; Pandey et al. “Plant Regeneration from Leaf and HypocotylExplants of Glycine wightii (W. and A.) VERDC. var. longicauda” (1992)Japan J. Breed. 42:1-5; and Shetty et al. “Stimulation of In Vitro ShootOrganogenesis in Glycine max (Merrill.) by Allantoin and Amides” (1992)Plant Science 81:245-251; U.S. Pat. No. 5,024,944, to Collins et al.;and U.S. Pat. No. 5,008,200, to Ranch et al., the disclosures of whichare hereby incorporated herein in their entirety by reference. Thus,another aspect is to provide cells which upon growth and differentiationproduce soybean plants having the physiological and morphologicalcharacteristics of soybean variety XB39AE12.

Soybean seeds, plants, and plant parts of variety XB39AE12 may becleaned and/or treated. The resulting seeds, plants, or plant partsproduced by the cleaning and/or treating process(es) may exhibitenhanced yield characteristics. Enhanced yield characteristics caninclude one or more of the following: increased germination efficiencyunder normal and/or stress conditions, improved plant physiology, growthand/or development, such as water use efficiency, water retentionefficiency, improved nitrogen use, enhanced carbon assimilation,improved photosynthesis, and accelerated maturation, and improveddisease and/or pathogen tolerance. Yield characteristics can furthermoreinclude enhanced plant architecture (under stress and non-stressconditions), including but not limited to early flowering, floweringcontrol for hybrid seed production, seedling vigor, plant size,internode number and distance, root growth, seed size, fruit size, podsize, pod or ear number, seed number per pod or ear, seed mass, enhancedseed filling, reduced seed dispersal, reduced pod dehiscence and lodgingresistance. Further yield characteristics include seed composition, suchas carbohydrate content, protein content, oil content and composition,nutritional value, reduction in anti-nutritional compounds, improvedprocessibility, and better storage stability.

Cleaning a seed or seed cleaning refers to the removal of impurities anddebris material from the harvested seed. Material to be removed from theseed includes but is not limited to soil, and plant waste, pebbles, weedseeds, broken soybean seeds, fungi, bacteria, insect material, includinginsect eggs, larvae, and parts thereof, and any other pests that existwith the harvested crop. The terms cleaning a seed or seed cleaning alsorefer to the removal of any debris or low quality, infested, or infectedseeds and seeds of different species that are foreign to the sample.

Treating a seed or applying a treatment to a seed refers to theapplication of a composition to a seed as a coating or otherwise. Thecomposition may be applied to the seed in a seed treatment at any timefrom harvesting of the seed to sowing of the seed. The composition maybe applied using methods including but not limited to mixing in acontainer, mechanical application, tumbling, spraying, misting, andimmersion. Thus, the composition may be applied as a powder, acrystalline, a ready-to-use, a slurry, a mist, and/or a soak. For ageneral discussion of techniques used to apply fungicides to seeds, see“Seed Treatment,” 2d ed., (1986), edited by K. A Jeffs (chapter 9),herein incorporated by reference in its entirety. The composition to beused as a seed treatment can comprise one or more of a pesticide, afungicide, an insecticide, a nematicide, an antimicrobial, an inoculant,a growth promoter, a polymer, a flow agent, a coating, or anycombination thereof. General classes or family of seed treatment agentsinclude triazoles, anilides, pyrazoles, carboxamides, succinatedehydrogenase inhibitors (SDHI), triazolinthiones, strobilurins, amides,and anthranilic diamides. In some examples, the seed treatment comprisestrifloxystrobin, azoxystrobin, metalaxyl, metalaxyl-m, mefenoxam,fludioxinil, imidacloprid, thiamethoxam, thiabendazole, ipconazole,penflufen, sedaxane, prothioconazole, picoxystrobin, penthiopyrad,pyraclastrobin, xemium, Rhizobia spp., Bradyrhizobium spp. (e.g., B.japonicum), Bacillus spp. (e.g., B. firmus, B. pumilus, B. subtilis),lipo-chitooligosaccharide, clothianidin, cyazapyr, rynaxapyr, abamectin,and any combination thereof. In some examples the seed treatmentcomprises trifloxystrobin, metalaxyl, imidacloprid, Bacillus spp., andany combination thereof. In some examples the seed treatment comprisespicoxystrobin, penthiopyrad, cyazapyr, ranaxapyr, and any combinationthereof. In some examples, the seed treatment improves seed germinationunder normal and/or stress environments, early stand count, vigor,yield, root formation, nodulation, and any combination thereof. In someexamples seed treatment reduces seed dust levels, insect damage,pathogen establishment and/or damage, plant virus infection and/ordamage, and any combination thereof.

Soybean seeds, plants, and plant parts of variety XB39AE12 may be usedor processed for food, animal feed, or a raw material(s) for industry.Seeds from variety XB39AE12 can be crushed, or a component of the seedscan be extracted in order to make a plant product, such as proteinconcentrate, protein isolate, soybean hulls, meal, flour, or oil for afood or feed product. Methods of producing a plant product, such asprotein concentrate, protein isolate, soybean hulls, meal, flour, or oilfor a food or feed product are provided. Also provided are the proteinconcentrate, protein isolate, soybean hulls, meal, flour, or oilproduced by the methods.

Oil extracted from soybeans is used for cooking oil, margarine, andsalad dressings. Soybean oil has a typical composition of 11% palmitic,4% stearic, 25% oleic, 50% linoleic, and 9% linolenic fatty acidcontent. Industrial uses of soybean oil, which is typically subjected tofurther processing, include ingredients for paints, plastics, fibers,detergents, cosmetics, lubricants, and biodiesel fuel. Soybean oil maybe split, inter-esterified, sulfurized, epoxidized, polymerized,ethoxylated, or cleaved. To produce oil, the harvested soybeans arecracked, adjusted for moisture content, rolled into flakes, and then theoil is solvent-extracted. The oil extract is refined, optionally blendedand/or hydrogenated. Some soybean varieties have modified fatty acidprofiles and can be used to produce soybean oil with a modified fattyacid composition. Oil with 3% or less linolenic acid is classified aslow linolenic oil, oil with less than 1% linolenic acid is classified asultra low linolenic oil. Oil with 70% or higher of oleic acid isclassified as high oleic oil.

Soybeans are also used as a food source for both animals and humans.Soybeans are widely used as a source of protein for animal feed. Thefibrous hull is removed from whole soybean and the oil is extracted. Theremaining meal is a combination of carbohydrates and approximately 50%protein. This remaining meal is heat treated under well-establishedconditions and ground in a hammer mill. Soybean is a predominant sourcefor livestock feed components.

In addition to soybean meal, soybean can be used to produce soy flour.Soy flour refers to defatted soybeans where special care was takenduring desolventizing to minimize protein denaturation and to retain ahigh nitrogen solubility index (NSI) in making the flour. Soy flour isthe typical starting material for production of soy concentrate and soyprotein isolate. Defatted soy flour is obtained from solvent extractedflakes, and contains less than 1% oil. Full-fat soy flour is made fromwhole beans and contains about 18% to 20% oil. Low-fat soy flour is madeby adding back some oil to defatted soy flour. The lipid content varies,but is usually between 4.5-9%. High-fat soy flour can also be producedby adding soybean oil to defatted flour at the level of 15%.Lecithinated soy flour is made by adding soybean lecithin to defatted,low-fat or high-fat soy flours to increase dispersibility and impartemulsifying properties.

For human consumption, soybean can be used to produce edible ingredientswhich serve as an alternative source of dietary protein. Common examplesinclude milk, cheese, and meat substitutes. Additionally, soybean can beused to produce various types of fillers for meat and poultry products.Vitamins and/or minerals may be added to make soy products nutritionallymore equivalent to animal protein sources as the protein quality isalready roughly equivalent.

DEPOSITS

Applicant has made a deposit of seeds of Soybean Variety XB39AE12 withthe American Type Culture Collection (ATCC), 10801 University Blvd.,Manassas, Va. 20110 USA, ATCC Deposit No. PTA-122606. The seedsdeposited with the ATCC on Oct. 12, 2015 were taken from the seed stockmaintained by Pioneer Hi-Bred International, Inc., 7250 NW 62^(nd)Avenue, Johnston, Iowa 50131 since prior to the filing date of thisapplication. Access to this seed stock will be available during thependency of the application to the Commissioner of Patents andTrademarks and persons determined by the Commissioner to be entitledthereto upon request. Upon allowance of any claims in the application,the Applicant will make the deposit available to the public pursuant to37 C.F.R. §1.808. This deposit of Soybean Variety XB39AE12 will bemaintained in the ATCC depository, which is a public depository, for aperiod of 30 years, or 5 years after the most recent request, or for theenforceable life of the patent, whichever is longer, and will bereplaced if it becomes nonviable during that period. Additionally,Applicant has or will satisfy all the requirements of 37 C.F.R.§§1.801-1.809, including providing an indication of the viability of thesample upon deposit. Applicant has no authority to waive anyrestrictions imposed by law on the transfer of biological material orits transportation in commerce. Applicant does not waive anyinfringement of their rights granted under this patent or under thePlant Variety Protection Act (7 USC 2321 et seq.).

All publications, patents, and patent applications mentioned in thespecification are indicative of the level of those skilled in the art towhich this invention pertains. All such publications, patents, andpatent applications are incorporated by reference herein for the purposecited to the same extent as if each was specifically and individuallyindicated to be incorporated by reference herein.

The foregoing invention has been described in detail by way ofillustration and example for purposes of clarity and understanding. Asis readily apparent to one skilled in the art, the foregoing are onlysome of the methods and compositions that illustrate the embodiments ofthe foregoing invention. It will be apparent to those of ordinary skillin the art that variations, changes, modifications, and alterations maybe applied to the compositions and/or methods described herein withoutdeparting from the true spirit, concept, and scope of the invention.

As used herein, the terms “comprises,” “comprising,” “includes,”“including,” “has,” “having,” “contains”, “containing,” “characterizedby” or any other variation thereof, are intended to cover anon-exclusive inclusion. For example, a composition, mixture, process,method, article, or apparatus that comprises a list of elements is notnecessarily limited to only those elements but may include otherelements not expressly listed or inherent to such composition, mixture,process, method, article, or apparatus. The transitional phrase“consisting of” excludes any element, step, or ingredient other thanthose recited except for impurities ordinarily associated therewith.When the phrase “consisting of” appears in a clause of the body of aclaim, rather than immediately following the preamble, it limits onlythe element set forth in that clause; other elements are not excludedfrom the claim as a whole. The transitional phrase “consistingessentially of” is used to define a composition, method or apparatusthat includes materials, steps, features, components, or elements, inaddition to those literally disclosed, provided that these additionalmaterials, steps, features, components, or elements do not materiallyaffect the basic characteristic(s).

Unless expressly stated to the contrary, “or” is used as an inclusiveterm. For example, a condition A or B is satisfied by any one of thefollowing: A is true (or present) and B is false (or not present), A isfalse (or not present) and B is true (or present), and both A and B aretrue (or present). The indefinite articles “a” and “an” preceding anelement or component are nonrestrictive regarding the number ofinstances (i.e., occurrences) of the element or component. Therefore “a”or “an” should be read to include one or at least one, and the singularword form of the element or component also includes the plural unlessthe number is obviously meant to be singular.

TABLE 1 Variety Description Information Current Variety Name XB39AE12Relative Maturity 3.9 Canadian Heat Units Herbicide Resistance GlyHarvest Standability 7 Emergence Score 88 Hypocotyl Score 99Phytophthora Gene 1K Phytophthora Field 4 Brown Stem Rot Iron Chlorosis3 Downy Mildew White Mold Sudden Death Syndrome 6 Cyst Nematode Race1Cyst Nematode Race2 Cyst Nematode Race3 88 Cyst Nematode Race5 CystNematode Race14 99 Aphid Antibosis 5 Charcoal Rot Drought 5 Root-knotSouthern Root-knot Peanut Stem Canker Genetic Frogeye Leaf Spot 66Frogeye LeafSpot Lab 33 Cercospora Field Chloride Sensitivity 33 CanopyWidth 5 Shattering 99 Height/Maturity 5 Plant Growth Habit Ind Oil/MealType % Protein @ 13% H2O 32 % Oil @ 13% H2O 19.6 Seed Size Score 8 SeedSize Range Flower Color P Pubescence Color L Hila Color BL Pod Color BRSeed Coat Luster D

TABLE 2 VARIETY COMPARISON DATA Variety1 Variety2 Statistic YIELD MATABSHGT LDGSEV SPLB SDS PROTN % OIL % FEY CRDC SHATTR EMGSC XB39AE12 93Y70Mean1 59.5 122.7 40.7 6.9 4 32.75 19.47 9 7.5 XB39AE12 93Y70 Mean2 57.8120 39.3 5.4 4 33.65 19.31 8 8 XB39AE12 93Y70 #Locs 28 10 3 6 1 4 4 2 1XB39AE12 93Y70 #Reps 38 12 4 7 1 4 4 2 2 XB39AE12 93Y70 #Years 2 1 1 2 11 1 1 1 XB39AE12 93Y70 SE Diff 0.94 0.91 0.33 0.85 0.406 0.174 1XB39AE12 93Y70 Prob 0.0875 0.0145 0.0572 0.1366 0.1118 0.4272 0.5XB39AE12 93Y72 Mean1 56.7 132.9 34.6 6.5 3383 31.21 19.78 5 4 XB39AE1293Y72 Mean2 56.4 130.7 41.6 6.1 2999 32.13 19.76 6 5.3 XB39AE12 93Y72#Locs 41 13 7 7 7 5 5 1 2 XB39AE12 93Y72 #Reps 86 26 13 12 7 5 5 2 3XB39AE12 93Y72 #Years 1 1 1 1 1 1 1 1 1 XB39AE12 93Y72 SE Diff 0.87 0.81.5 0.63 66.8 0.377 0.205 0.25 XB39AE12 93Y72 Prob 0.765 0.0189 0.00340.5934 0.0012 0.0713 0.9394 0.1257 XB39AE12 93Y82 Mean1 57.8 128.4 36.57 3383 4 31.95 19.52 5 4 9 7.5 XB39AE12 93Y82 Mean2 58.1 126.1 41.1 6.82762 5 32.66 19.31 5.5 6.8 7.5 8.5 XB39AE12 93Y82 #Locs 66 23 10 12 7 110 10 1 2 2 1 XB39AE12 93Y82 #Reps 116 38 17 17 7 1 10 10 2 3 2 2XB39AE12 93Y82 #Years 2 2 2 2 1 1 2 2 1 1 1 1 XB39AE12 93Y82 SE Diff0.62 0.64 1.27 0.48 51.9 0.32 0.217 0.75 0.5 XB39AE12 93Y82 Prob 0.61220.0012 0.0051 0.7998 0 0.0522 0.3493 0.1695 0.2048 XB39AE12 93Y91 Mean157.8 128.4 36.5 7.3 3388 4 31.89 19.77 5 4 9 7.5 XB39AE12 93Y91 Mean255.3 128.6 40.6 6.2 3068 4 33.99 19.51 7.5 7.3 8.5 8 XB39AE12 93Y91#Locs 63 23 10 11 6 1 10 10 1 2 2 1 XB39AE12 93Y91 #Reps 115 38 17 15 61 10 10 2 3 2 2 XB39AE12 93Y91 #Years 2 2 2 2 1 1 2 2 1 1 1 1 XB39AE1293Y91 SE Diff 0.77 0.6 0.66 0.3 85.4 0.227 0.133 0.25 0.5 XB39AE12 93Y91Prob 0.002 0.8399 0.0001 0.0046 0.0134 0 0.0846 0.0489 0.5 XB39AE1293Y92 Mean1 57.8 128.4 36.5 7.3 3383 4 32 19.61 5 4 9 7.5 XB39AE12 93Y92Mean2 56.5 128.8 42.9 6 3053 4 33.29 19.14 9 5 9 8 XB39AE12 93Y92 #Locs63 23 10 11 7 1 11 11 1 2 2 1 XB39AE12 93Y92 #Reps 112 38 17 15 7 1 1111 2 3 2 2 XB39AE12 93Y92 #Years 2 2 2 2 1 1 2 2 1 1 1 1 XB39AE12 93Y92SE Diff 0.68 0.57 0.94 0.45 59.5 0.368 0.223 1 0 XB39AE12 93Y92 Prob0.0623 0.5753 0.0001 0.0177 0.0015 0.0059 0.0624 0.5 1 XB39AE12 93Y93Mean1 56.7 132.9 34.6 7 3383 31.41 19.56 5 4 XB39AE12 93Y93 Mean2 51.4135.5 37.9 7 3101 33.25 18.77 9 5.3 XB39AE12 93Y93 #Locs 37 13 7 6 7 6 61 2 XB39AE12 93Y93 #Reps 79 26 13 10 7 6 6 2 3 XB39AE12 93Y93 #Years 1 11 1 1 1 1 1 1 XB39AE12 93Y93 SE Diff 1.12 0.5 0.55 0.22 76.3 0.61 0.3720.25 XB39AE12 93Y93 Prob 0 0.0002 0.001 1 0.0102 0.0296 0.087 0.1257XB39AE12 94Y01 Mean1 57.8 128.2 36.5 7.3 3383 4 32 19.61 5 4 9 7.5XB39AE12 94Y01 Mean2 55.3 129 41.7 5.7 3542 3 33.14 19.35 6 4.5 8.5 8XB39AE12 94Y01 #Locs 63 22 10 11 7 1 11 11 1 2 2 1 XB39AE12 94Y01 #Reps113 37 17 15 7 1 11 11 2 3 2 2 XB39AE12 94Y01 #Years 2 2 2 2 1 1 2 2 1 11 1 XB39AE12 94Y01 SE Diff 0.76 0.51 1.33 0.34 50.4 0.323 0.18 0.5 0.5XB39AE12 94Y01 Prob 0.0018 0.1013 0.0036 0.0008 0.0193 0.0057 0.18 0.50.5 XB39AE12 RJS38001 Mean1 56.6 132.9 34.6 7 3383 31.41 19.56 5 4XB39AE12 RJS38001 Mean2 54.7 132.3 40.3 5.9 3120 32.5 19.24 8.5 4.8XB39AE12 RJS38001 #Locs 38 13 7 6 7 6 6 1 2 XB39AE12 RJS38001 #Reps 8126 12 9 7 6 6 2 3 XB39AE12 RJS38001 #Years 1 1 1 1 1 1 1 1 1 XB39AE12RJS38001 SE Diff 0.96 0.43 0.82 0.37 46.7 0.507 0.283 0.25 XB39AE12RJS38001 Prob 0.0548 0.2431 0.0005 0.0341 0.0014 0.0844 0.3192 0.2048XB39AE12 RJS38010 Mean1 58.2 3.5 XB39AE12 RJS38010 Mean2 55.8 3 XB39AE12RJS38010 #Locs 3 1 XB39AE12 RJS38010 #Reps 6 2 XB39AE12 RJS38010 #Years1 1 XB39AE12 RJS38010 SE Diff 0.68 XB39AE12 RJS38010 Prob 0.0735XB39AE12 RJS39002 Mean1 56.6 132.9 34.6 7 3383 31.41 19.56 5 4 XB39AE12RJS39002 Mean2 53.3 131.9 39.9 6.4 3294 33.28 19.06 5 3.3 XB39AE12RJS39002 #Locs 38 13 7 6 7 6 6 1 2 XB39AE12 RJS39002 #Reps 81 26 13 10 76 6 2 3 XB39AE12 RJS39002 #Years 1 1 1 1 1 1 1 1 1 XB39AE12 RJS39002 SEDiff 0.97 0.52 1.03 0.91 74.3 0.55 0.201 0.75 XB39AE12 RJS39002 Prob0.0018 0.0737 0.0023 0.5487 0.2793 0.0196 0.0548 0.5 XB39AE12 RJS39005Mean1 56.7 132.9 34.6 6.5 3383 31.41 19.56 5 4 XB39AE12 RJS39005 Mean256.2 130.9 39.4 6.1 2956 32.41 19.1 8.5 5.8 XB39AE12 RJS39005 #Locs 4113 7 7 7 6 6 1 2 XB39AE12 RJS39005 #Reps 88 26 13 12 8 6 6 2 3 XB39AE12RJS39005 #Years 1 1 1 1 1 1 1 1 1 XB39AE12 RJS39005 SE Diff 1.15 0.890.99 0.47 60.4 0.461 0.167 0.25 XB39AE12 RJS39005 Prob 0.6468 0.04830.0029 0.3955 0.0004 0.0841 0.041 0.0903 XB39AE12 RJS39007 Mean1 56.7132.9 34.6 6.5 3383 31.41 19.56 5 4 XB39AE12 RJS39007 Mean2 55.9 132.437.8 6 3156 33.52 19.11 6 4.8 XB39AE12 RJS39007 #Locs 41 13 7 7 7 6 6 12 XB39AE12 RJS39007 #Reps 87 26 13 12 7 6 6 2 3 XB39AE12 RJS39007 #Years1 1 1 1 1 1 1 1 1 XB39AE12 RJS39007 SE Diff 0.99 0.71 1.03 0.24 103.30.611 0.324 1.25 XB39AE12 RJS39007 Prob 0.399 0.5391 0.0223 0.08630.0711 0.0182 0.2293 0.656

TABLE 3 Soybean SSR Marker Set SAC1006 SATT129 SATT243 SATT334 SAC1611SATT130 SATT247 SATT335 SAC1634 SATT131 SATT249 SATT336 SAC1677 SATT133SATT250 SATT338 SAC1699 SATT142 SATT251 SATT339 SAC1701 SATT144 SATT255SATT343 SAC1724 SATT146 SATT256 SATT346 SAT_084 SATT147 SATT257 SATT347SAT_090 SATT150 SATT258 SATT348 SAT_104 SATT151 SATT259 SATT352 SAT_117SATT153 SATT262 SATT353 SAT_142-DB SATT155 SATT263 SATT355 SAT_189SATT156 SATT264 SATT356 SAT_222-DB SATT165 SATT265 SATT357 SAT_261SATT166 SATT266 SATT358 SAT_270 SATT168 SATT267 SATT359 SAT_271-DBSATT172 SATT270 SATT361 SAT_273-DB SATT175 SATT272 SATT364 SAT_275-DBSATT181 SATT274 SATT367 SAT_299 SATT183 SATT279 SATT369 SAT_301 SATT186SATT280 SATT373 SAT_311-DB SATT190 SATT282 SATT378 SAT_317 SATT191SATT284 SATT380 SAT_319-DB SATT193 SATT285 SATT383 SAT_330-DB SATT195SATT287 SATT385 SAT_331-DB SATT196 SATT292 SATT387 SAT_343 SATT197SATT295 SATT389 SAT_351 SATT199 SATT299 SATT390 SAT_366 SATT202 SATT300SATT391 SAT_381 SATT203 SATT307 SATT393 SATT040 SATT204 SATT314 SATT398SATT042 SATT212 SATT319 SATT399 SATT050 SATT213 SATT321 SATT406 SATT092SATT216 SATT322 SATT409 SATT102 SATT219 SATT326 SATT411 SATT108 SATT221SATT327 SATT412 SATT109 SATT225 SATT328 SATT413 SATT111 SATT227 SATT330SATT414 SATT115 SATT228 SATT331 SATT415 SATT122 SATT230 SATT332 SATT417SATT127 SATT233 SATT333 SATT418 SATT420 SATT508 SATT583 SATT701 SATT421SATT509 SATT584 SATT708-TB SATT422 SATT510 SATT586 SATT712 SATT423SATT511 SATT587 SATT234 SATT429 SATT512 SATT590 SATT240 SATT431 SATT513SATT591 SATT242 SATT432 SATT514 SATT594 SATT433 SATT515 SATT595 SATT436SATT517 SATT596 SATT440 SATT519 SATT597 SATT441 SATT522 SATT598 SATT442SATT523 SATT601 SATT444 SATT524 SATT602 SATT448 SATT526 SATT608 SATT451SATT529 SATT613 SATT452 SATT533 SATT614 SATT454 SATT534 SATT617 SATT455SATT536 SATT618 SATT457 SATT537 SATT628 SATT460 SATT540 SATT629 SATT461SATT544 SATT630 SATT464 SATT545 SATT631 SATT466 SATT546 SATT632-TBSATT467 SATT548 SATT633 SATT469 SATT549 SATT634 SATT470 SATT550 SATT636SATT471 SATT551 SATT640-TB SATT473 SATT552 SATT651 SATT475 SATT555SATT654 SATT476 SATT556 SATT655-TB SATT477 SATT557 SATT656 SATT478SATT558 SATT660 SATT479 SATT565 SATT661-TB SATT480 SATT566 SATT662SATT487 SATT567 SATT665 SATT488 SATT568 SATT666 SATT491 SATT569 SATT667SATT492 SATT570 SATT672 SATT493 SATT572 SATT675 SATT495 SATT573 SATT677SATT497 SATT576 SATT678 SATT503 SATT578 SATT680 SATT506 SATT581 SATT684SATT507 SATT582 SATT685

TABLE 4 BREEDING HISTORY FOR XB39AE12 Bi-parental cross F1 growoutharvested in bulk F2 modified single seed descent F3 single plantselections made Progeny row yield test Purification - single plantsselected Regional yield testing Purification - individual plant rowsharvested and advanced Purification - individual plant rows bulkedtogether Advanced yield testing Bulk breeder's seed increase Foundationseed production Elite yield testing

What is claimed is:
 1. A plant, a plant part, or a seed of soybeanvariety XB39AE12, representative seed of said soybean variety XB39AE12having been deposited under ATCC Accession Number PTA-122606.
 2. Asoybean seed obtained by introducing a transgene into soybean varietyXB39AE12, wherein a plant grown from said seed otherwise comprises allof the physiological and morphological characteristics of soybeanvariety XB39AE12, representative seed of said soybean variety XB39AE12having been deposited under ATCC Accession Number PTA-122606.
 3. Theseed of claim 2, wherein the transgene confers a trait selected from thegroup consisting of male sterility, site-specific recombination, abioticstress tolerance, altered phosphorus, altered antioxidants, alteredfatty acids, altered essential amino acids, altered carbohydrates,herbicide resistance, insect resistance, and disease resistance, whereina plant grown from said seed otherwise comprises all of thephysiological and morphological characteristics of soybean varietyXB39AE12.
 4. A soybean plant, or a part thereof, produced by growing theseed of claim
 1. 5. A soybean plant, or a part thereof, produced bygrowing the seed of claim 2, wherein said plant otherwise comprises allof the physiological and morphological characteristics of soybeanvariety XB39AE12.
 6. A method for developing a second soybean plantcomprising applying plant breeding techniques to a first soybean plant,or parts thereof, wherein said first soybean plant is the soybean plantof claim 1, and wherein application of said techniques results indevelopment of said second soybean plant.
 7. A method for producingsoybean seed comprising crossing two soybean plants and harvesting theresultant soybean seed, wherein at least one soybean plant is thesoybean plant of claim
 1. 8. An F1 soybean seed produced by the methodof claim
 7. 9. A soybean plant, or a part thereof, produced by growingsaid seed of claim
 8. 10. A method for developing a second soybean plantin a soybean plant breeding program comprising applying plant breedingtechniques to a first soybean plant, or parts thereof, wherein saidfirst soybean plant is the soybean plant of claim 9, and whereinapplication of said techniques results in development of said secondsoybean plant.
 11. A method of producing a soybean plant comprising alocus conversion, the method comprising introducing a locus conversioninto the plant of claim 1, wherein said locus conversion provides atrait selected from the group consisting of male sterility,site-specific recombination, abiotic stress tolerance, alteredphosphorus, altered antioxidants, altered fatty acids, altered essentialamino acids, altered carbohydrates, herbicide resistance, insectresistance, and disease resistance.
 12. A herbicide resistant soybeanplant produced by the method of claim 11, wherein said plant otherwisecomprises all of the physiological and morphological characteristics ofsoybean variety XB39AE12.
 13. A disease resistant soybean plant producedby the method of claim 11, wherein said plant otherwise comprises all ofthe physiological and morphological characteristics of soybean varietyXB39AE12.
 14. An insect resistant soybean plant produced by the methodof claim
 11. 15. The soybean plant of claim 14, wherein the locusconversion comprises a transgene encoding a Bacillus thuringiensis (Bt)endotoxin, wherein said plant otherwise comprises all of thephysiological and morphological characteristics of soybean varietyXB39AE12.
 16. A soybean plant, or a part thereof, expressing all thephysiological and morphological characteristics of soybean varietyXB39AE12, representative seed of said soybean variety XB39AE12 havingbeen deposited under ATCC Accession Number PTA-122606.
 17. A methodcomprising isolating nucleic acids from a plant, a plant part, or a seedof soybean variety XB39AE12, analyzing said nucleic acids to producedata, and recording the data for XB39AE12.
 18. The method of claim 17,wherein the data is recorded on a computer readable medium.
 19. Themethod of claim 17, further comprising using the data for crossing,selection, or advancement decisions in a breeding program.
 20. Themethod of claim 17, wherein the data is a nucleic acid sequence, amarker profile, a haplotype, or any combination thereof.